Sweet, got it figured out, the start button was what I needed to know. And thanks for the explanation of IPS. Games are small enough, I'm not too concerned about SMB sharing anyway.
Here's the weird thing... at first I thought you were wrong... cuz if I push 'start' on my el-cheapo MadCatz controller in the main xsnes9x screen, nothing happens at all. There's nothing wrong with the start button itself tho, it works fine in everything else (including within the SNES games). Before I came back and posted you were crazy tho, I figured I'd try with my old official big MS controller. Sure enough, if I plug it in as controller 1, it works. (If I leave it as controller 2, the start button works, but that seems to be the only button that works).
Weird & annoying, I guess I should buy one of the real MS small controllers if I want the best of both worlds. The version of flashbios on my x3 chip only works with the MS controller too, so maybe it's related.