I think in older versions of iTunes it was called "Ring Tones" and after the introduction of notification tones it was changed to simply "Tones." Even an iPad can use the tones for things other than the ringer.
I also think that the solution to this problem is simply a corrupt media library. I eventually discovered that toggling all the check marks for each type of media and then syncing seemed to clear up all problems. So, if you have music set to sync, uncheck that box. If you have movies set to not sync, check that box (but you can uncheck all movies so nothing syncs). Wait for the sync to finish, clearing out all media from the iPod/iPad/iPhone. Then just re-set the sync checkmarks back to their original state and sync again. All of your sync settings should be preserved (so if you are syncing specific albums, for example, they will still be selected when you re-activate music syncing).
Doing this should re-build the iOS media library and correct all problems. I was having difficulty finishing my sync, podcasts were missing, music wouldn't finish, TV shows were being ignored, etc. Once I cleared all synced content and re-synced, everything was fine.
I don't think the issue has to do with iOS 5. I only noticed it when I disconnected my iPhone while it was syncing via USB (I thought it was syncing via WiFi). The corrupt library seems to stem from suddenly interrupted syncs, which would be compounded if you get inpatient and force the sync to stop when it says, "Waiting for items to copy."