Anything you have updated recently or any such changes you can think of?
I haven't used snes9x under Linux before, but I tried it some just now, and if you run it via terminal, do you get any hints there? What kind of sound buffer size is it showing and whatnot.
I tried for no particular reason to run it with -eightbit and that would for some reason slow down the 'playback' quite a bit... Probably not as drastic as what you describe but either way, any hints in the terminal? Using any particular switches?
I know that's not what you want exactly, but may I suggest that you try bsnes? It's an accuracy based SNES emulator. It's available at roslin's overlay (layman -a roslin).