Alright, after digging around, I found the REAL ini file and made changes, and so far, it's responded to them just fine, but now I've got another weird problem with the options screen-
When I try to change controls for "Input (General)",suddenly the menu is almost completely off screen, and this happens regardless of what game I load. However, options for "Input (This machine)" is perfectly visible. What's going on? Also, how do I setup shaders per game?