try to configure your gamepad with this
http://www.tomshardware.com/forum/33080-63-windows-gamepads
also, you may want to visit your controller manufacturers website to check for any drivers or software. using the official software (if there is any) will be easiest although typically only the big names have software associated with them.
if that doesnt work then you can use a 3rd party one such as "xpadder" or "xinput"