Are you sure the particular files are not being copied to iPod? Recheck! They may be under a totally different section (such as audio books or simply in the main library section)
Some links about audiobook formats & issues:
http://aldoblog.com/blog/494 http://aldoblog.com/blog/471 http://www.gudlyf.com/archives/2004/...diobook-issue/ http://www.audiobooksforfree.com/xMP3/default.asp