Going to a bootable chip solution is always the best. Thinking about finally ditching my no-solder for a real chip this summer. In the mean time though, you could try the SwapMagic fix CD. It's made for using with the SM2.0 BootCD and requires an additional swap for the TOC load and Media Switch, but it should get around the problems if it lies in the game's code.
If it ain't broke don't try to fix it! But, hell if you can tweak that bastard just a little bit more....hehehe.