I'm also having re-sync problems. Around 800 files of the 5000 file on my ipod get re-synced evey time even though they ahve not changed at all. I don't have a full analysis yet but it seems to always be the same files.
I'm having that problem too, and I think I know what's causing it for me. When I'm tagging audio files, if the group's name starts with the word "The" I move it to the end (e.g. "The Beatles" becomes "Beatles, The"). I've noticed that my iPod always sorts and displays them in their original form ("The Beatles"), which surprised and annoyed me a little but didn't cause any real trouble with MC11.
But MC12 seems to be confused by this, because it wants to re-download all of those files every time I do a sync. And if I let it, they end up duplicated on my iPod, so that after a few syncs its hard drive fills up.
The only workaround I've found is to initialize my iPod before every sync, forcing MC to spend hours downloading everything again (but only once!).
