Controller not really registering

[yoshi_star10]

1. Are you interested in using TeamViewer? No
2. What is your OS? Example Vista, XP, Mac OSX, etc. Windows 7
3. What is your browser? Firefox 6
4. Post a link to one game you are having problems with. Earthbound-SNES
5. What Play Mode is causing the problem? Example ArcadeOX Score, Java Full, etc. ArcadeOX
6. Has it ever worked correctly before? Yes on other games but this is my first time playing this one
7. Describe the problem.
   I have an XBOX 360 Afterglow controller, When i go into the game to set up the controller input, it registers the button presses there, and it sets the button for whichever one i pushed. I pressed ok, but when I try and start the game, (its going through its little game intro screen) It doesnt seem to know im pressing buttons. I push them all but it wont do anything.