Incredible. I spent a day trying to figure out why the header of my site gets all messed up randomly for some pages.
I'm using W3 Total Cache and the Ubermenu plugin. Suspecting that Ubermenu was the culprit was the last thing in my mind. Did a lot of troubleshooting and what not.
Then when I did a line by line compare of the source code of a "bad" file vs a good file served by total cache, I noticed that there is no difference at all.
Then inspecting the header area I realized that the Ubermenu CSS isn't being loaded at all!!! Don't have a solution for now, but the long term solution is to drop Ubermenu and just write a function myself to populate the menus.
Less plugins, less headaches ...