Thanks for the tip, I actually tried similar to that. I just didn't back anything up (I have Time Machine running, just incase). I thought it might be some corrupt mp3's but, I have tried this with matched m4a's as well with the same results.
I made a ton of changes with match turned off, turned it back on and some were updated properly; but most were reverted. I have checked the drive they are stored on for permissions and verified the disk itself, no problems.
I have all other devices turned off, and acutally unlinked all my accounts yesterday.
I've been using Match since release, and have never had this problem. I'm honestly thinking its this new version of iTunes. Its really the only thing that has changed that I can see that could possibly cause the problem.
I have also just put a ticket into Apple about this.