I had this problem when I switched from Bluetooth to USB, using a PS3 controller mapped as Xbox360 one.
My controller scheme simply went mad. I restarted game, still buggy. Resetted computer, buggy. And as you, I had to re-calibrate to make it work.

But that just happens if I do this while with game opened. If I close it, plug the USB and start game, that does not happen. Probably windows' fault. (Or game's, dunno. Easier to blame Microsoft lol).