I just tried the .desktop trick on 1.20. It worked fine for Earthbound and had 3 smaller screens to the left for Chrono Trigger and Super Mario RPG. If I try it from the command line, it still just freezes solid.
So it appears that snes9x gets progressively less functional as the Cacko ROM gets newer. At least for me, that is.
Edit: Well, Earthbound was working fine. When I tried it again after trying the other ROMs, it started doing the small screen thing. After exiting and trying again, it appears to have frozen solid again.
I've run both NAND and RAM diagnostics through the service menu, but both turned out fine. Any suggestions would be much appreciated.
Edit... again: Everything (except Mario RPG, but that was expected) just magically started working again. Didn't do anything but reboot a few times after it froze.