I use a wired XBox360 controller and it works properly, but with a wireless Xbox360 controller I don't know...
FB Alpha uses the DirectInput API to receive the inputs from a game controller and this may be "the root of the problem"... the XInput is the specific API to use the Xbox360 controllers under Windows and it's not supported by the current FB Alpha.
PS: probably this will not able to solve your problem, but you can try with the FB Alpha X86 versions.