I haven't had this problem under Win2K running "generic" drivers that windows loaded with my Cyborg and it holds its settings between games/reboots.
However a friend of mine under Win2K with generic drivers has to calibrate every time he starts the game with his EVO, though it stays in calibration once its set.
My stick is hyper-sensitive under AH2, making the game unplayable, even with its settings very low.