diff --git a/lib/galaxy/web/framework/helpers/__init__.py b/lib/galaxy/web/framework/helpers/__init__.py
index d024c8f1ede..3c6b9a4d638 100644
--- a/lib/galaxy/web/framework/helpers/__init__.py
+++ b/lib/galaxy/web/framework/helpers/__init__.py
@@ -44,7 +44,7 @@ def js( *args ):
     TODO: This has a hardcoded "?v=2" to defeat caching. This should be done
           in a better way.
     """
-    return "\n".join( [ javascript_include_tag( "/static/scripts/" + name + ".js?v=2" ) for name in args ] )
+    return "\n".join( [ javascript_include_tag( "/static/scripts/" + name + ".js?v=3" ) for name in args ] )
     
 # Hashes
 
diff --git a/static/scripts/galaxy.base.js b/static/scripts/galaxy.base.js
index d4ab140c51f..b7905a40367 100644
--- a/static/scripts/galaxy.base.js
+++ b/static/scripts/galaxy.base.js
@@ -242,44 +242,50 @@ function replace_big_select_inputs(min_length) {
             // Get refresh vals.
             var refresh_vals = select_elt.attr('refresh_on_change_values');
             if (refresh_vals !== undefined)
-                refresh_vals = refresh_vals.split(",")
-            text_input_elt.keyup( function( e ) 
+                refresh_vals = refresh_vals.split(",");
+                
+            // Function that attempts to refresh based on the value in the text element.
+            var try_refresh_fn = function() 
             {
-                if ( ( e.keyCode == 13 ) && // Return Key
-                     ( return_key_pressed_for_autocomplete == true ) ) // Make sure return key was for autocomplete.
+                //
+                // If value entered can be matched to value, do so and refresh by submitting parent form.
+                //
+                
+                // Get new value and see if it can be matched.
+                var cur_value = text_input_elt.attr('value');
+                var new_value = select_mapping[cur_value];
+                if (new_value !== null && new_value !== undefined) 
                 {
-                    //
-                    // If value entered can be matched to value, do so and refresh by submitting parent form.
-                    //
-                    
-                    // Get new value and see if it can be matched.
-                    var cur_value = text_input_elt.attr('value');
-                    var new_value = select_mapping[cur_value];
-                    if (new_value !== null && new_value !== undefined) 
+                    // Do refresh if new value is refresh value or if there are no refresh values.
+                    refresh = false;
+                    if (refresh_vals !== undefined)
                     {
-                        // Do refresh if new value is refresh value or if there are no refresh values.
-                        refresh = false;
-                        if (refresh_vals !== undefined)
-                        {
-                            for (var i= 0; i < refresh_vals.length; i++ )
-                                if (new_value == refresh_vals[i])
-                                {
-                                    refresh = true;
-                                    break;
-                                }
-                        }
-                        else
-                            // Refresh for all values.
-                            refresh = true;
+                        for (var i= 0; i < refresh_vals.length; i++ )
+                            if (new_value == refresh_vals[i])
+                            {
+                                refresh = true;
+                                break;
+                            }
+                    }
+                    else
+                        // Refresh for all values.
+                        refresh = true;
 
-                        if (refresh)
-                        {
-                            text_input_elt.attr('value', new_value);
-                            text_input_elt.parents('form').submit();
-                        }
+                    if (refresh)
+                    {
+                        text_input_elt.attr('value', new_value);
+                        text_input_elt.parents('form').submit();
                     }
                 }
+            };
+            
+            // Attempt refresh if (a) result event fired by autocomplete (indicating autocomplete occurred) or (b) on keyup (in which
+            // case a user may have manually entered a value that needs to be refreshed).
+            text_input_elt.bind("result", try_refresh_fn);
+            text_input_elt.keyup( function(e) {
+                try_refresh_fn();
             });
+
         }
     });
 }
diff --git a/static/scripts/packed/galaxy.base.js b/static/scripts/packed/galaxy.base.js
index 0c3947a59ca..e0d4af50c35 100644
--- a/static/scripts/packed/galaxy.base.js
+++ b/static/scripts/packed/galaxy.base.js
@@ -1 +1 @@
-$(document).ready(function(){replace_big_select_inputs()});$.fn.makeAbsolute=function(a){return this.each(function(){var b=$(this);var c=b.position();b.css({position:"absolute",marginLeft:0,marginTop:0,top:c.top,left:c.left,right:$(window).width()-(c.left+b.width())});if(a){b.remove().appendTo("body")}})};function ensure_popup_helper(){if($("#popup-helper").length===0){$("<div id='popup-helper'/>").css({background:"white",opacity:0,zIndex:15000,position:"absolute",top:0,left:0,width:"100%",height:"100%"}).appendTo("body").hide()}}function attach_popupmenu(b,d){var a=function(){d.unbind().hide();$("#popup-helper").unbind("click.popupmenu").hide()};var c=function(g){$("#popup-helper").bind("click.popupmenu",a).show();d.click(a).css({left:0,top:-1000}).show();var f=g.pageX-d.width()/2;f=Math.min(f,$(document).scrollLeft()+$(window).width()-$(d).width()-20);f=Math.max(f,$(document).scrollLeft()+20);d.css({top:g.pageY-5,left:f});return false};$(b).click(c)}function make_popupmenu(c,b){ensure_popup_helper();var a=$("<ul id='"+c.attr("id")+"-menu'></ul>");$.each(b,function(f,e){if(e){$("<li/>").html(f).click(e).appendTo(a)}else{$("<li class='head'/>").html(f).appendTo(a)}});var d=$("<div class='popmenu-wrapper'>");d.append(a).append("<div class='overlay-border'>").css("position","absolute").appendTo("body").hide();attach_popupmenu(c,d)}function make_popup_menus(){jQuery("div[popupmenu]").each(function(){var c={};$(this).find("a").each(function(){var b=$(this).attr("confirm"),d=$(this).attr("href"),e=$(this).attr("target");c[$(this).text()]=function(){if(!b||confirm(b)){var g=window;if(e=="_parent"){g=window.parent}else{if(e=="_top"){g=window.top}}g.location=d}}});var a=$("#"+$(this).attr("popupmenu"));make_popupmenu(a,c);$(this).remove();a.addClass("popup").show()})}function array_length(b){if(b.length){return b.length}var c=0;for(var a in b){c++}return c}function naturalSort(i,g){var n=/(-?[0-9\.]+)/g,j=i.toString().toLowerCase()||"",f=g.toString().toLowerCase()||"",k=String.fromCharCode(0),l=j.replace(n,k+"$1"+k).split(k),e=f.replace(n,k+"$1"+k).split(k),d=(new Date(j)).getTime(),m=d?(new Date(f)).getTime():null;if(m){if(d<m){return -1}else{if(d>m){return 1}}}for(var h=0,c=Math.max(l.length,e.length);h<c;h++){oFxNcL=parseFloat(l[h])||l[h];oFyNcL=parseFloat(e[h])||e[h];if(oFxNcL<oFyNcL){return -1}else{if(oFxNcL>oFyNcL){return 1}}}return 0}function replace_big_select_inputs(a){if(typeof jQuery().autocomplete=="undefined"){return}if(a===undefined){a=20}$("select").each(function(){var b=$(this);if(b.find("option").length<a){return}var c=b.attr("value");var d=$("<input type='text' class='text-and-autocomplete-select'></input>");d.attr("size",40);d.attr("name",b.attr("name"));d.attr("id",b.attr("id"));d.click(function(){var j=$(this).attr("value");$(this).attr("value","Loading...");$(this).showAllInCache();$(this).attr("value",j);$(this).select()});var i=[];var h={};b.children("option").each(function(){var k=$(this).text();var j=$(this).attr("value");i.push(k);h[k]=j;h[j]=j;if(j==c){d.attr("value",k)}});if(c==""||c=="?"){d.attr("value","Click to Search or Select")}i=i.sort(naturalSort);var g={selectFirst:false,autoFill:false,mustMatch:false,matchContains:true,max:1000,minChars:0,hideForLessThanMinChars:false};d.autocomplete(i,g);b.replaceWith(d);var e=function(){var k=d.attr("value");var j=h[k];if(j!==null&&j!==undefined){d.attr("value",j)}else{if(c!=""){d.attr("value",c)}else{d.attr("value","?")}}};d.parents("form").submit(function(){e()});$(document).bind("convert_dbkeys",function(){e()});if(b.attr("refresh_on_change")=="true"){var f=b.attr("refresh_on_change_values");if(f!==undefined){f=f.split(",")}d.keyup(function(m){if((m.keyCode==13)&&(return_key_pressed_for_autocomplete==true)){var l=d.attr("value");var k=h[l];if(k!==null&&k!==undefined){refresh=false;if(f!==undefined){for(var j=0;j<f.length;j++){if(k==f[j]){refresh=true;break}}}else{refresh=true}if(refresh){d.attr("value",k);d.parents("form").submit()}}}})}})}function async_save_text(d,f,e,a,c,h,i,g,b){if(c===undefined){c=30}if(i===undefined){i=4}$("#"+d).live("click",function(){if($("#renaming-active").length>0){return}var l=$("#"+f),k=l.text(),j;if(h){j=$("<textarea></textarea>").attr({rows:i,cols:c}).text(k)}else{j=$("<input type='text'></input>").attr({value:k,size:c})}j.attr("id","renaming-active");j.blur(function(){$(this).remove();l.show();if(b){b(j)}});j.keyup(function(n){if(n.keyCode===27){$(this).trigger("blur")}else{if(n.keyCode===13){var m={};m[a]=$(this).val();$(this).trigger("blur");$.ajax({url:e,data:m,error:function(){alert("Text editing for elt "+f+" failed")},success:function(o){l.text(o);if(b){b(j)}}})}}});if(g){g(j)}l.hide();j.insertAfter(l);j.focus();j.select();return})}function init_history_items(d,a,c){var b=function(){try{var e=$.jStore.store("history_expand_state");if(e){for(var g in e){$("#"+g+" div.historyItemBody").show()}}}catch(f){$.jStore.remove("history_expand_state")}if($.browser.mozilla){$("div.historyItemBody").each(function(){if(!$(this).is(":visible")){$(this).find("pre.peek").css("overflow","hidden")}})}d.each(function(){var j=this.id;var h=$(this).children("div.historyItemBody");var i=h.find("pre.peek");$(this).find(".historyItemTitleBar > .historyItemTitle").wrap("<a href='javascript:void(0);'></a>").click(function(){if(h.is(":visible")){if($.browser.mozilla){i.css("overflow","hidden")}h.slideUp("fast");if(!c){var k=$.jStore.store("history_expand_state");if(k){delete k[j];$.jStore.store("history_expand_state",k)}}}else{h.slideDown("fast",function(){if($.browser.mozilla){i.css("overflow","auto")}});if(!c){var k=$.jStore.store("history_expand_state");if(k===undefined){k={}}k[j]=true;$.jStore.store("history_expand_state",k)}}return false})});$("#top-links > a.toggle").click(function(){var h=$.jStore.store("history_expand_state");if(h===undefined){h={}}$("div.historyItemBody:visible").each(function(){if($.browser.mozilla){$(this).find("pre.peek").css("overflow","hidden")}$(this).slideUp("fast");if(h){delete h[$(this).parent().attr("id")]}});$.jStore.store("history_expand_state",h)}).show()};if(a){b()}else{$.jStore.init("galaxy");$.jStore.engineReady(function(){b()})}}$(document).ready(function(){$("a[confirm]").click(function(){return confirm($(this).attr("confirm"))});if($.fn.tipsy){$(".tooltip").tipsy({gravity:"s"})}make_popup_menus()});
\ No newline at end of file
+$(document).ready(function(){replace_big_select_inputs()});$.fn.makeAbsolute=function(a){return this.each(function(){var b=$(this);var c=b.position();b.css({position:"absolute",marginLeft:0,marginTop:0,top:c.top,left:c.left,right:$(window).width()-(c.left+b.width())});if(a){b.remove().appendTo("body")}})};function ensure_popup_helper(){if($("#popup-helper").length===0){$("<div id='popup-helper'/>").css({background:"white",opacity:0,zIndex:15000,position:"absolute",top:0,left:0,width:"100%",height:"100%"}).appendTo("body").hide()}}function attach_popupmenu(b,d){var a=function(){d.unbind().hide();$("#popup-helper").unbind("click.popupmenu").hide()};var c=function(g){$("#popup-helper").bind("click.popupmenu",a).show();d.click(a).css({left:0,top:-1000}).show();var f=g.pageX-d.width()/2;f=Math.min(f,$(document).scrollLeft()+$(window).width()-$(d).width()-20);f=Math.max(f,$(document).scrollLeft()+20);d.css({top:g.pageY-5,left:f});return false};$(b).click(c)}function make_popupmenu(c,b){ensure_popup_helper();var a=$("<ul id='"+c.attr("id")+"-menu'></ul>");$.each(b,function(f,e){if(e){$("<li/>").html(f).click(e).appendTo(a)}else{$("<li class='head'/>").html(f).appendTo(a)}});var d=$("<div class='popmenu-wrapper'>");d.append(a).append("<div class='overlay-border'>").css("position","absolute").appendTo("body").hide();attach_popupmenu(c,d)}function make_popup_menus(){jQuery("div[popupmenu]").each(function(){var c={};$(this).find("a").each(function(){var b=$(this).attr("confirm"),d=$(this).attr("href"),e=$(this).attr("target");c[$(this).text()]=function(){if(!b||confirm(b)){var g=window;if(e=="_parent"){g=window.parent}else{if(e=="_top"){g=window.top}}g.location=d}}});var a=$("#"+$(this).attr("popupmenu"));make_popupmenu(a,c);$(this).remove();a.addClass("popup").show()})}function array_length(b){if(b.length){return b.length}var c=0;for(var a in b){c++}return c}function naturalSort(i,g){var n=/(-?[0-9\.]+)/g,j=i.toString().toLowerCase()||"",f=g.toString().toLowerCase()||"",k=String.fromCharCode(0),l=j.replace(n,k+"$1"+k).split(k),e=f.replace(n,k+"$1"+k).split(k),d=(new Date(j)).getTime(),m=d?(new Date(f)).getTime():null;if(m){if(d<m){return -1}else{if(d>m){return 1}}}for(var h=0,c=Math.max(l.length,e.length);h<c;h++){oFxNcL=parseFloat(l[h])||l[h];oFyNcL=parseFloat(e[h])||e[h];if(oFxNcL<oFyNcL){return -1}else{if(oFxNcL>oFyNcL){return 1}}}return 0}function replace_big_select_inputs(a){if(typeof jQuery().autocomplete=="undefined"){return}if(a===undefined){a=20}$("select").each(function(){var d=$(this);if(d.find("option").length<a){return}var j=d.attr("value");var b=$("<input type='text' class='text-and-autocomplete-select'></input>");b.attr("size",40);b.attr("name",d.attr("name"));b.attr("id",d.attr("id"));b.click(function(){var k=$(this).attr("value");$(this).attr("value","Loading...");$(this).showAllInCache();$(this).attr("value",k);$(this).select()});var e=[];var g={};d.children("option").each(function(){var l=$(this).text();var k=$(this).attr("value");e.push(l);g[l]=k;g[k]=k;if(k==j){b.attr("value",l)}});if(j==""||j=="?"){b.attr("value","Click to Search or Select")}e=e.sort(naturalSort);var f={selectFirst:false,autoFill:false,mustMatch:false,matchContains:true,max:1000,minChars:0,hideForLessThanMinChars:false};b.autocomplete(e,f);d.replaceWith(b);var i=function(){var l=b.attr("value");var k=g[l];if(k!==null&&k!==undefined){b.attr("value",k)}else{if(j!=""){b.attr("value",j)}else{b.attr("value","?")}}};b.parents("form").submit(function(){i()});$(document).bind("convert_dbkeys",function(){i()});if(d.attr("refresh_on_change")=="true"){var c=d.attr("refresh_on_change_values");if(c!==undefined){c=c.split(",")}var h=function(){var m=b.attr("value");var l=g[m];if(l!==null&&l!==undefined){refresh=false;if(c!==undefined){for(var k=0;k<c.length;k++){if(l==c[k]){refresh=true;break}}}else{refresh=true}if(refresh){b.attr("value",l);b.parents("form").submit()}}};b.bind("result",h);b.keyup(function(k){h()})}})}function async_save_text(d,f,e,a,c,h,i,g,b){if(c===undefined){c=30}if(i===undefined){i=4}$("#"+d).live("click",function(){if($("#renaming-active").length>0){return}var l=$("#"+f),k=l.text(),j;if(h){j=$("<textarea></textarea>").attr({rows:i,cols:c}).text(k)}else{j=$("<input type='text'></input>").attr({value:k,size:c})}j.attr("id","renaming-active");j.blur(function(){$(this).remove();l.show();if(b){b(j)}});j.keyup(function(n){if(n.keyCode===27){$(this).trigger("blur")}else{if(n.keyCode===13){var m={};m[a]=$(this).val();$(this).trigger("blur");$.ajax({url:e,data:m,error:function(){alert("Text editing for elt "+f+" failed")},success:function(o){l.text(o);if(b){b(j)}}})}}});if(g){g(j)}l.hide();j.insertAfter(l);j.focus();j.select();return})}function init_history_items(d,a,c){var b=function(){try{var e=$.jStore.store("history_expand_state");if(e){for(var g in e){$("#"+g+" div.historyItemBody").show()}}}catch(f){$.jStore.remove("history_expand_state")}if($.browser.mozilla){$("div.historyItemBody").each(function(){if(!$(this).is(":visible")){$(this).find("pre.peek").css("overflow","hidden")}})}d.each(function(){var j=this.id;var h=$(this).children("div.historyItemBody");var i=h.find("pre.peek");$(this).find(".historyItemTitleBar > .historyItemTitle").wrap("<a href='javascript:void(0);'></a>").click(function(){if(h.is(":visible")){if($.browser.mozilla){i.css("overflow","hidden")}h.slideUp("fast");if(!c){var k=$.jStore.store("history_expand_state");if(k){delete k[j];$.jStore.store("history_expand_state",k)}}}else{h.slideDown("fast",function(){if($.browser.mozilla){i.css("overflow","auto")}});if(!c){var k=$.jStore.store("history_expand_state");if(k===undefined){k={}}k[j]=true;$.jStore.store("history_expand_state",k)}}return false})});$("#top-links > a.toggle").click(function(){var h=$.jStore.store("history_expand_state");if(h===undefined){h={}}$("div.historyItemBody:visible").each(function(){if($.browser.mozilla){$(this).find("pre.peek").css("overflow","hidden")}$(this).slideUp("fast");if(h){delete h[$(this).parent().attr("id")]}});$.jStore.store("history_expand_state",h)}).show()};if(a){b()}else{$.jStore.init("galaxy");$.jStore.engineReady(function(){b()})}}$(document).ready(function(){$("a[confirm]").click(function(){return confirm($(this).attr("confirm"))});if($.fn.tipsy){$(".tooltip").tipsy({gravity:"s"})}make_popup_menus()});
\ No newline at end of file