Argh, I'm a dumbass. It just now clicked that "regs" contains the SuperFX registers, but "cpu.regs" corresponds to the S-CPU registers. Grah.
ETA: Hmm, no. No, hooking up the S-CPU IRQ didn't seem to actually affect anything.
ETA2: Dammit, I reimplemented RAM and ROM buffering based on bsnes's spec, and it also isn't affecting anything. At least we're narrowing things down here.
ETA3: byuu, do you have a copy of this? bsnes_v046_wip13.tar.bz2