I was having some issue with the AD auth and menu bars. I would change to a custom menu bar for an admin group and it didn't show up for me (at first). I was going to open a ticket but it took me a couple days to find the time, but viola, the menu bar I wanted was there now! I have a feeling it had something to do with cache. Try clearing your browsers cache and the web cache from the settings page (top right corner, just below the menu bar).
Netlogix is right or at least on the right track. I checked our support log and one of them mentioned to clear your browser's cache.
Give that a try and post back.
Also, did you download the two hotfixes for 10.1.1? They are in your customer portal.