Let me ask you this:
Do you have one of the "new" iPods? The ones with the dock connector and the backlit buttons?
At this time, I believe that what you are describing is a bug in the iPod Operating System (v2.0), not in MC9.
I had a "classic" iPod, which worked great with MC9. Since I've traded up for my new "3rd Generation" iPod, some songs, which played perfectly before, exhibit the same bug that you're describing.
The general consensus at iPodlounge.com is that it's a problem with the iPod's OS, not with our uploading software.
Can you please check the "About" screen of your iPod and tell us what it says? If it says 2.0, this is a known bug (well, known by us... not so much acknowledged by Apple).
If your about screen says 1.3 or earlier I would greatly appreciate an email (kurtsipod at hotmail dot com). I'm very happy and comfy thinking it's a new 2.0 bug... I'd hate to hear that it's an MC bug.