I just worked through this problem on my Droid. I'm posting in case anyone else is having the same issues.

The Problem:
This weekend I was bashing my head against the wall trying to get music onto my Droid. I copied 6ish albums over and the phone recognized them without any problems. Then I tried transferring about 1250 songs over and when I went to the Music player, only about half of them were recognized. I was able to see all of them with my file manager on the phone. I tried all sorts of things: deleting and copying all the files again, syncing with doubletwist, taking all the songs out of folders and copying them in. None of it worked.

The Solution:
Rather than transferring all 1250 songs at one time, I broke it up into three transfers. I would hook my phone up to the computer, transfer about 400 songs, disconnect it, and let the Music player scan and recognize the new songs. Then I repeated the process 2 more times. Now it finally sees all my songs! Definitely only a workaround, but at least I can listen to music now!