Hi Beth,
Sorry but I have no explanation for that and am not able to reproduce that problem. I just did a clean install of mojoPortal 2.4.0.2 then added the skin art31-green from our extra skins which is an older one that I know uses treeview. Then I downloaded the zip I sent you from my sent mail extracted it and deployed it to this installation and nothing changed in the menu.
I've also deployed it to the demo site but the demo site doesn't have any skins using TreeView, all newer skins use FlexMenu, so I uploaded the art31-green skin to the demo site and it works fine with TreeView.
I keep a copy of the source code exactly as it is for each release and the changes to add the option to disable the file uploaded were applied directly to only 2 files WebConfigSettings.cs and jQueryFileUpload.cs and re-compiled to create the patched dll I sent. There were no other changes and definitely no changes to any treeview control in over 18 months much less in this patched version.
Best,
Joe