It’s probably the database limit as explained above. Scroll down Albums or Artists and see if it stops before the end of the alphabet.
But:
Are all the files .mp3, .flac, .ogg or .wav ?
The Fuze will not play .m4a files (iTunes files), and it won’t show any file it can’t play.
If you are using iTunes you can highlight the .m4a files, right-click and Create mp3 Version. But then you’ll have to find them wherever iTunes hides them…