Higan seems picky about controllers. My trusty Gravis Game Pad Pro works but it ignores my Gravis Xterminator. There's a new release (.98) that came out last month, so try grabbing that from the Emulation Lair and see if it makes a difference. If not there's always ZSNES and SNES9x.
I've downloaded Higan .97, and for some reason my controller(Hyperkin GN6 USB)will not work with it. When I try to configure it only acceepts inputs from the keyboard and mouse. I can confirm the controller works with the latest version of the Kega Fusion emulator. Any thoughts or tips?