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