Can the files that are not showing up be played by the Zune software? You might try this...
Go to Options and set the option for adding a file to the library when added to the playlist. Open Windows File Explorer and select all (or a few for a test) of the files that are not showing up. Either right-click and select Play (if your default player is the Zune) or drag them to the Playlist window in the Zune software.
Now that they are in the playlist window, they should be added to your library.
This is a bit drastic but you might also try...
Remove all monitored directories. The default ripping directory cannot be removed. Everything should drop out of your library. If not, select delete but don't delete from your hard drive. Plug in the device and sync. This will set a baseline.
Add back in a single monitored directory and let it search. Select those same options for adding deleted files and files from another library. If the files are still not showing up, I would be leaning towards reinstalling the Zune software and letting it rebuild your library from scratch. This is also a bit drastic but much better than not being able to get new content on the device.
You may also want to make sure the files are not flagged to be skipped in the Sync Results report. That can be found in the navigation node named for your device in the Zune software.
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