Well, after I had those problems, I went back to iTunes for the past few weeks, and today, I reinitialized for MC.
Now I can't duplicate it. I re-initialized, and synced a few playlists that I was having problems with, making sure (before I synced for the first time) to check that the "Set Upload Volume.....Replay Gain" option was checked correctly. So after the songs transferred, I put on some headphones, and it seemed to be working. I do have 2 questions though.
1. Does 'Sound Check' have an effect on songs that MC sends the Replay Gain data for?
2. Is it possible that before (when I was having problems) that maybe the Volume Adjustment options weren't checked the first time I transferred my library over to the iPod, and since the songs were never copied over again, with the option checked, that was what was causing the problem?
Sorry if my post is confusing, I always have problems describing these computer related issues on message boards.
Thanks for listening though.
--Matt