Here's a bug report of another GB desync bug (possibly 2 of them, actually, which Bag of Magic Food ran into), which is in alpha 5 of the rerecording VBA.
I recorded the following VMV file:
http://nvdata.pilif.ch/rmwtest.zip
for the ROM "Rockman World (J).gb"
To play it back correctly, you need to do the following:
* Set the sound to 44KHz instead of 22KHz
* Pause the game, choose to play the movie, then hit Frame Advance until the frame counter says 50, and unpause.
Try skipping either or both of these steps, and the movie will desync a little after frame 3100, or sometimes it will desync later. (If it plays correctly, the only times I get hit are around around frame 5000 and frame 5100.) So, obviously frame advance is still causing the game to play differently than it should, and the sound sample rate is also causing an unwanted difference. (Maybe the sound sample rate reliance cannot be avoided, in which case it would be nice if the movie saved the sound settings it was recorded with, but the frame advance problem is definitely a bug.)
(On the other hand, recording for GBA games is flawless as far as I can tell.)