This is odd to me, After setting up the stick in windows, I have only had to recalibrate in AH after patching, as the game seems to lose the calibration.  I haven't had any problems with it losing calibration in WinXP, or AH between patches.  
Did you use the driver disk that came with it, or download the new one from Saitek?  I am told the new one is junk.
Blackwulf