I've been experiencing all kinds of crazy stuff with my Apple gear that is synced to one another — iPhone, iPad, MacBook Pro, iMac, Apple TV.
For the past two weeks, syncing takes forever, and certain files are missing in iTunes. I believe that this is especially true for longer term users who are carrying the baggage of multiple old operating systems in their cache — as Apple has been updating protocols for the new stuff that's coming.
Last night I restored by my iPhone and iPad to their original settings and did not auto populate anything. Everything fresh, from scratch.
Today everything works like a charm.
This may not be a bad thing to do for y'alls before the 19th when iOS 6 gets downloaded.