After beating ALttP and getting quite far in Earthbound, I set my ROMs to automatically open with snes9x. All in game save-files and save states are deleted. The icons for the ROMs display the snes9x logo, and opening the files with the original logos (which are still around, separately) with snes9x displays a black screen with yellow text instead of the usual white saying something around being corrupted. Please help!!

easiest fix is to not do it that way. open up snes9x as per normal and life will be fine.

otherwise, you're going to need to create a shortcut to snes9x and set the working directory properly, and then modify your file association to use the shortcut instead of the snes9x executable.

fyi, the "files with the original logos" are the sram and savestate files. you can't open them directly.

technical: path issues suck. setting an association without making sure the launching executable can find its working directory makes things break horribly.

edit: at a glance, win32.cpp seems to explicitly account for startup dir not being snes9x dir. going to need to dig deeper (or have someone actually familiar with the code look).

How?

Check the paths set up in snes9x, do they point to the correct location?

Correct. S9x does not care about the current working directory, it always uses the executable directory for relative paths.