I know this is an old thread but I never closed it out and detailed the solution. Anyway, iTunes uses a built in database to keep track of tags. When you update tags in itunes they are supposed to go to both the file as well as the database. This doesn't always happen so when you update a tag in iTunes, then play that song outside of iTunes it could have the old tag information which was the issue with the tags not being in sync. They were in iTunes but not the song itself.
I used MediaMonkey to sync up all of the tags with itunes and the file itself then went back into iTunes to update the built in DB. I had to select on each song individually to get iTunes to see the new tags so I wrote a small script to scroll through each song (5500 or so)so iTunes could update its database. Once everything was synced up in the file as well as itunes I resynced using iSyncr...problem solved.
Coincidentally this was the same issue for the Album art. I had artwork stored in itunes but not in the song file so...Mediamonkey to the rescue again. Updated all of the album art that was missing or was out of sync then went back into itunes to clean it up.
Once everything was fixed iSyncr worked like a champ...and still does.