Well I have to say I have not heard of any thing like that before. check the following:
> open up note pad and make a text document like this:
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put the cursor in the middle and watch it. If it moves its your os. I would at least rule that out.
> Make sure the other joysticks are not plugged in, that is the check box in the controllers setup in snes9x Up at the top. Only have player 1 connected.
>also try having all joysticks unchecked to see what happened's.
>if you have not make sure to try this on other games, if you only tried it on one game it could be that game.
>if you feel up to it, unplug the keyboard during play to see if its stops. If it does, its the keyboard that is doing it. You will need to shut down you computer with your mouse to plug it back in. FYI. Plugging a keyboard back in to your system if its turned on is not recommended. Consider this at your own risk.
Other then that my friend you may just have to go with zsnes.