Snes9x.com

It's my only gripe with this emulator. It works great, but if you don't already have the controller plugged into the USB part before opening whatever game it doesn't detect it. So you can't plug it in afterward and have it register.

This wasn't a big issue before, but now my controller is acting funny. It seems like if I leave the controller inactive for about a minute it stops being detected. and I like to multitask. It only takes about 10 seconds to hit the hotkey for a savestate, X out, reload the game, then hit the hotkey for loading the savestate, but it's very inconvenient when I have to do this frequently.

I don't know if the controller is going bad, or it's something with the USB port, but it's getting annoying.

FWIW, I have the same issue with Xbox 360 and One controllers. If they aren't on when I fire up the emulator (MAME and FCEUX have the same issue) then they don't work. I have to close the emulator then relaunch for the controllers to work.

In s9x you can manually trigger a recheck with "Input->Detect Gamepad Changes"