Hey byuu, you mentioned that you largely took Gambatte's code piecemeal to try to get SGB games working. Could this have anything to do with the issues you were seeing?

http://speeddemosarchive.com/kb/Super_Game_Boy_timing

Edit: Oh, hey, the proper values are already listed on... *shudder*... overclocked.org:

Quote
Clock Speed: 4.194304 MHz (4.295454 MHz for Super GB)
Horiz Sync: 9198 KHz (9420 KHz for Super GB)
Vert Sync: 59.73 Hz (61.17 Hz for Super GB)