Search the World Cup 2006 forum. If you add something like [Hid-Compliant Game Controller] in the file somewhere everything works fine. Whats great is in Windows Vista Fifa 2007 supports Xbox 360 Controller to its full extent--rumble included.
which drivers are you using, if you have microsoft drivers it should work fine with no problems. but if you are using the XBCD drivers, then you need to make a custom profile for the controller. and also you need to alter the devdata.dat. i could make them for you, if you tell me what is the gamepad's name in the "game controller" config menu in the control panle of windows.