I'm having the same issue too, but I'm not sure exactly what's going on. In my case, it seems to be something to do with iTunes Match.
I have an artist with say 5 albums that I ripped from my CDs. They've played fine for 5 years on all my iPods. Then iTunes Match came around and I realized I had ripped these CDs all those years ago at 128k, so I decided to let Match do it's thing to upgrade them to 256k. I deleted the 5 albums from my library, and downloaded them from Match.
Everything appears to be there and plays fine in iTunes, but when I sync these 5 albums back to my iPods, about 20% of the songs stop part way through and skip to the next track. I have tested playback on an iPhone 4, iPod Touch 4, and a Nano 6, and they all do the same thing on the same songs.
As a test, I deleted one of the problem tracks and re-downoaded it from Match, and it now plays fine on all devices. That makes me suspect that I'm getting corrupted files from Match sometimes.
In my case, I know I can simply re-rip the CDs, but I would like to know what's going on and find out how to prevent it.