I'm not sure if the rebuild process works with 2.0. I don't have any MP3s on my player at the moment, but I could roll back to 2.0, encode some, and try it. Would that be valuable test data for you, or should I just wait for a fix?
Speaking of patches.. I tried to apply the patch you linked earlier, but my Windows copy of "patch" behaves very oddly.
I tried "patch -p3 < whatever_the_patch_was_called.txt", and it just created a subdirectory called "-p3"
I was too lazy to send the files over to a Linux box with a 'real' patch tool.