Did you ever come up with a solution for this? I have the same problem, and I don't have enough control over the server to research it. I also have a problem with the module action menus not displaying as well with the same javascript messagebox, so I'm guessing it has something to do with the AJAX implementation. Any additonal info you can provide would be awesome!

I did perform a recursive sync... I don't think it is really a matter of the data being in the Files and Folders tables, so much as there being a problem with the AJAX library that is pushed down. When I click on the plus to expand the Folder tree in File Manager or when I mouse-over the action menu on a container a javascript t have any problems. The admin of the problem server says there is nothing special installed on that server that would cause this issue (like a third-party AJAX library or http compression tool.) Obviously there is something different, so any suggestions would be great.