It always appeared to be that you could just plug the controller in (ie. XNA).
Ok, you said all games minimize themselves with the controller plugged in and software installed?
Strange, sounds to me like a driver bug of sorts, I suggest you search (and ask) at the Microsoft Support website, since minimizing windows isn't exactly what ought to happen.
Btw, BC can't make use of gamepads (atleast, not that I remember, though some synaps' are firing that Defiant made something for that).