I've used Linux for a while except for gaming, so in terms of emulation I'm a recent convert from Windows and ZSNES. My computer runs openSUSE x86_64, with 2GB RAM, an Athlon II 2.9 GHz dual-core processor, and Radeon HD 5670 graphics. Today I decided to build SNES9x and use it with the same three roms (Star Fox, Super Mario World, Super Mario All Stars) that I used with ZSNES with no problem.
This problem only happens when using the SNES9x-gtk interface. All three roms work fine with the command-line snes9x.
When playing a game -- and ONLY when playing a game, not when the game is paused or there is no game -- my entire screen, not just the SNES9x window, flashes to black for a split second. I have no idea what could be causing this. Here is the error message:
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/usr/bin/xdg-screensaver: line 564: dcop: command not found

So I installed a package containing DCOP, and now the message is:
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ERROR: Couldn't attach to DCOP server!
Here is the ROM information for Super Mario World, although I don't think it will matter since it happens with every ROM I tired:
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Name: SUPER MARIOWORLD
Speed: 20/SlowROM
Map: LoROM
Type: 02
Contents: ROM+RAM+BAT
ROM Size: 4Mbits
Calculated Size: 4
SRAM Size: 16Kbits
Header Checksum: A0DA
Checksum Compliment: 5F25
Actual Checksum: A0DA
Video: NTSC 60Hz
CRC32: B19ED489
Revision: 1.0