A few possibilities:
Do you have your iPod set to ignore unchecked songs?
Is everything in your library music that is playable on the iPod? You might have a video or a PDF or something that will show up in iTunes but can't be moved to the iPod.
In general, though, I wouldn't obsess about 2 missing songs. It's like that number on your phone bill that you know you didn't call, but then you call it and you remember that you did in fact call it, and now you've called it twice. You'll probably find that the "missing" songs are things that you couldn't put on the iPod anyway, or things that you wouldn't want there.