Thanks for that. I made an XML file that inverted all the arrow keys with keyhelper so that when I play SNES without a joystick the down arrow moves my little guy down instead of up. The weird thing was changing the direction keys around using the export of the SNES9X keys method would work for some of the directions but not all of them (I think a direct swap of the export numbers makes it so that you can only walk left and down, never right and up).
I haven't had a chance to try your fix yet since I'm at work and can't really have Chrono bopping around on my screen, but I figured it had to be several things are fighting to interpret my direction keys at once and I imagine your script is the key to the fix.