What generation iPod are you using?
Use the forum search feature and look for "ipod."
The iPod library that Steven uses for MusicBee / iPod interaction isn't being developed any longer. iPods with 4th Generation (and possibly 5th) still work fine with MB, but versions later than that will have issues.
After re-reading your post, I wonder if the problem is the "format" or the iPod's firmware. The iPod can certainly read MP3s, so I wonder what format you're using. With your iPod connected, launch MB and go to Edit \ Preferences \ Devices. There you can set "on-the-fly conversion" to MP3, or some other formats, which can be read by the iPod.
Let us know how you make out.