Take a look at this thread if you haven't seen it
http://www.gnutellaforums.com/open-discussion-topics/36230-how-transfer-music-my-ipod-itunes.html
Although why M4A files shoud play and not mp3 is a bit of a mystery to me.
Will they load into the iTunes Library and not play or not load into iTunes atall?
Which version of iTunes are you using?
There are a small number of mp3s I have not been able to load into iTunes and I trash them ..but its only a few....