I imagine you using just a single MIDI cable, connecting the MIDI OUT from the SB (joystick/MIDI adapter) to the SC-55's MIDI IN port, and there are no return connections involved?
Well, actually... I've been assuming that the SC-55 would connect the same way as the MT-32. That is, In->Out, and Out->In. (I later read somewhere that one of the connections wasn't necessary, but I could never remember which one, so I kept connecting both - as long as it worked, why fiddle with it?
But, yes, this seems to have been the problem. I omit the MIDI IN part of the cable and the games don't lag anymore. Brilliant. Thank you for not assuming too much about a stupid layman's do's and don'ts!
Yes, I feel silly now for not trying this earlier, going out of my way to find more and more far-fetched solutions. But in my defense, the MT-32 has no problems with having both cables plugged in, and the same goes for the USB interface.
I still find that the notes get stuck briefly when I pause a MIDI file in Windows, or when I exit KQ6. However, the songs seem to play fine now: no more strange-sounding chords outside the Castle of the Crown for example. So it seems both problems have been solved. Thanks again!