diff --git a/lib/galaxy/tools/__init__.py b/lib/galaxy/tools/__init__.py
index 77f72677bb3..c83a650ec33 100755
--- a/lib/galaxy/tools/__init__.py
+++ b/lib/galaxy/tools/__init__.py
@@ -154,8 +154,24 @@ class ToolBox( object, Dictifiable ):
             # This will cover cases where the Galaxy administrator manually edited one or more of the tool panel
             # config files, adding or removing locally developed tools or workflows.  The value of integrated_tool_panel
             # will be False when things like functional tests are the caller.
+            self.fix_integrated_tool_panel_dict()
             self.write_integrated_tool_panel_config_file()
 
+    def fix_integrated_tool_panel_dict( self ):
+        # HACK: instead of fixing after the fact, I suggest some combination of:
+        #  1) adjusting init_tools() and called methods to get this right
+        #  2) redesigning the code and/or data structure used to read/write integrated_tool_panel.xml
+        for key, value in self.integrated_tool_panel.iteritems():
+            if key.startswith( 'section_' ):
+                for section_key, section_value in value.elems.iteritems():
+                    if section_value is None:
+                        if section_key.startswith( 'tool_' ):
+                            tool_id = section_key[5:]
+                            value.elems[section_key] = self.tools_by_id.get( tool_id )
+                        elif section_key.startswith( 'workflow_' ):
+                            workflow_id = section_key[9:]
+                            value.elems[section_key] = self.workflows_by_id.get( workflow_id )
+
     def init_tools( self, config_filename ):
         """
         Read the configuration file and load each tool.  The following tags are currently supported: