diff --git a/lib/galaxy/tools/__init__.py b/lib/galaxy/tools/__init__.py
index 37d33d0b73a..f330e3f2947 100755
--- a/lib/galaxy/tools/__init__.py
+++ b/lib/galaxy/tools/__init__.py
@@ -295,7 +295,7 @@ class ToolBox( object ):
                 self.load_workflow_tag_set( sub_elem, elems )
             elif sub_elem.tag == 'label':
                 self.load_label_tag_set( sub_elem, elems )
-        if key not in panel_dict and section.elems:
+        if key not in panel_dict:
             panel_dict[ key ] = section
     def load_tool( self, config_file, guid=None ):
         """
diff --git a/lib/galaxy/web/controllers/admin_toolshed.py b/lib/galaxy/web/controllers/admin_toolshed.py
index 5b8c97b812e..55af5b533db 100644
--- a/lib/galaxy/web/controllers/admin_toolshed.py
+++ b/lib/galaxy/web/controllers/admin_toolshed.py
@@ -499,18 +499,9 @@ class AdminToolshed( AdminGalaxy ):
                 metadata = repository.metadata
                 repository_tools_tups = get_repository_tools_tups( trans.app, metadata )
                 guids_to_activate = [ repository_tool_tup[1] for repository_tool_tup in repository_tools_tups ]
-                # Undelete the tool_version for each guid.
+                # Make sure we have a tool_version for each guid.
                 for guid_to_activate in guids_to_activate:
-                    tool_version = get_tool_version( trans.app, guid_to_activate )
-                    if tool_version:
-                        if tool_version.deleted:
-                            # This should not happen as we are currently not marking tool versions as deleted
-                            # upon deactivation.  We may decide to eliminate the tool_version.deleted column
-                            # at some point, but we'll keep it for now in case we decide its useful.
-                            tool_version.deleted = False
-                            trans.sa_session.add( tool_version )
-                            trans.sa_session.flush()
-                    else:
+                    if not get_tool_version( trans.app, guid_to_activate ):
                         # We're somehow missing a tool_version, so create a new one.
                         tool_version = trans.model.ToolVersion( tool_id=guid_to_activate, tool_shed_repository=repository )
                         trans.sa_session.add( tool_version )
diff --git a/templates/root/tool_menu.mako b/templates/root/tool_menu.mako
index 220fb0c8522..1fd501885fd 100644
--- a/templates/root/tool_menu.mako
+++ b/templates/root/tool_menu.mako
@@ -365,22 +365,25 @@
                         ${render_workflow( key, val, False )}
                     %elif key.startswith( 'section' ):
                         <% section = val %>
-                        <div class="toolSectionTitle" id="title_${section.id}">
-                            <span>${section.name}</span>
-                        </div>
-                        <div id="${section.id}" class="toolSectionBody">
-                            <div class="toolSectionBg">
-                                %for section_key, section_val in section.elems.items():
-                                    %if section_key.startswith( 'tool' ):
-                                        ${render_tool( section_val, True )}
-                                    %elif section_key.startswith( 'workflow' ):
-                                        ${render_workflow( section_key, section_val, True )}
-                                    %elif section_key.startswith( 'label' ):
-                                        ${render_label( section_val )}
-                                    %endif
-                                %endfor
+                        ## Render the section only if it is not empty.
+                        %if section.elems:
+                            <div class="toolSectionTitle" id="title_${section.id}">
+                                <span>${section.name}</span>
                             </div>
-                        </div>
+                            <div id="${section.id}" class="toolSectionBody">
+                                <div class="toolSectionBg">
+                                    %for section_key, section_val in section.elems.items():
+                                        %if section_key.startswith( 'tool' ):
+                                            ${render_tool( section_val, True )}
+                                        %elif section_key.startswith( 'workflow' ):
+                                            ${render_workflow( section_key, section_val, True )}
+                                        %elif section_key.startswith( 'label' ):
+                                            ${render_label( section_val )}
+                                        %endif
+                                    %endfor
+                                </div>
+                            </div>
+                        %endif
                     %elif key.startswith( 'label' ):
                         ${render_label( val )}
                     %endif