Hey guys,
Aye, this is most likely an iPod problem, caused by a change in the Portalplayer that's inside it.
My old Gen2 iPod, running 1.2.6, did not have this problem.
My new Gen3 iPod, running 2.0, and now 2.0.1, has this problem.
This problem seems to manifest only in songs that I've um... borrowed... from friends. Songs that come from CDs that me or my friends have personally ripped don't exhibit this problem.
Apparently, the new Portalplayer is very picky about the data it streams out. One too many "irregularities" and it either won't play the song or will stop playback and advance to the next song.
My only advice at this time is to remember which songs display this bug and use MC9's included Media Editor to convert to .wav and then back to .mp3. Doing this will eliminate whatever irregularities are in the file and encode it as a brand new file with a reliable encoder. I've had 100% success with this fix so far.
Pain in the butt, aye, but if the song's important to you, the 3 or 4 minutes it takes to decode/re-encode it will be worth it.