An iPod will skip over songs that it can't play. For example, if you try a 24 bit / 48 kHz WAV file or AIFF file the iPod will display the file but skip over it when you try to play it (an iPod can play a 24/48 ALAC file). I would suspect that a corrupted file would also have the same behavior.
Delete the problem files from the iPod and upload fresh versions. And make sure they're files they iPod can play (bit depth, sample rate, format).