You might want to try a Restore of your phone.
I am having the same problem with iTunes (currently 10.6.1 (7)). Every time I sync my iPhone 3GS, about a dozen Mono Beatles tunes are re-copied to the phone, even though they are already there. They are from boxed sets of Beatles CD's I purchased years ago. Each Mono cut from an early Beatles album has "[Mono]" appended to the title. They are all encoded in AAC, low complexity, mono, 160kbps. They were encoded with iTunes 6.0.2, Quicktime 7.0.4.
I agree it appears to be an iTunes bug.
Does anyone know... Is there a way to do something equivalent to "deleting prefs" for a flaky app... except somehow resetting all the music sync data for the iPhone instead?
My only thought is I might try a Restore of the iPhone. I'd have to be sure to get all my photos etc. off of it first, then Restore through iTunes and reload everything. I know this "last resort" option is there for fixing many problems, but I don't want to try it until I'm sure it's not just an iTunes 10.6 bug in the first place.
You might want to try a restore though. Just make sure you have all your photos, videos etc. off of there and backed up somewhere first. You do it by choosing "Restore" from the itunes window when your phone is plugged into the computer (it can't work over Wifi).
Please post back your results if you try it. Thanks.