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