The problem is that, iPods/iPhones are somewhat picky about the encoding of the MP3 file, so they won't play everything that iTunes does. It won't even sync. iTunes actually points out this in the file's information, saying that the file was "Encoded with: Unknown".
Still, the best solution is 2 clicks away. Within iTunes, select those musics, then right-click and click "Create MP3 version". You'll get a new set of musics that were encoded with iTunes that your device will happily sync.
