yep this happened to me to so I gave up ;;
I think they have to be a certain size and stuff maybe? the one I can't seem to get into iTunes is a bit bigger than the other one that actually went in, but I haven't converted it again to test this out myself..
and some seem to go into iTunes, but appear black in my iPod ..I'm not sure why this happens either and again I gave up.
another one would go into iTunes and just not go onto my iPod with this problem I used iTunes to convert it and it worked *shrug*
it's a big pita ^_^;;