I am running Snes9x on Windows, and my usual key setting is: WASD for directions, numpad keys for the buttons: B:2, A:6, Y:4, X:8
However A, W and Num4 doesn't want to work together. When I changed the direction keys or the button to something else, it worked fine, but the combination of these 3 seems to have a bug in it. Problem is, I'm kind of used to this control for a long time already.
Weird things with Input configuration
Re: Weird things with Input configuration
Given the distance between them it seems like this would be unlikely, but you might be running into an issue of key rollover. See here: https://en.wikipedia.org/wiki/Rollover_(key)