Store per game configuration?

[Shonumi]

Don't know if that was ever fixed. If you are using the JITIL recompiler, try switching to the JIT recompiler. The interpreter should not have any issues with that, but that will be slow. You could also verify the MD5 hash to check the intregrity of your game dump (if it doesn't match up with verified dumps such as those on Redump.org, you should redump the game from your disc until the hashes match).