Re: Emulators on Ubuntu somewhat lacking.. ?
Ah I see. If the one highlighted green is activated, then yes you're using it. You're fully up to date, yes? You could try Options/Preferences/Display in SNES9x and click "Use [however many] threads for filtering and scaling". I have a dual core CPU so I use 2 threads. Could help.
I can't imagine why you're getting this problem though. Are you using the latest driver (v.195.36.24) in System/Administration/Nvidia X Server Settings? Do you have Compiz effects enabled, such as desktop cube etc?
AMD Phenom X4 945, 4Gb Crucial 800Mhz DDR2 RAM, 1Tb SATA III HDD, nVidia 9800GT 512Mb