Never had the calibration problem myself, but I used to have the problem Jekyll mentions of having to wake the rudder pedals. (Saitek X36 USB with CH Pro Pedals USB here.)
I don't know if you noticed, but everytime you unplug your rudder pedals and plug them again, they go to another ID spot. I think that's why the joystick assignments go to hell. Maybe if you manually assign ID#2 to the CH Pro Pedals everytime, you won't loose the joystick axis assignments.
When I bought my X36 and my rudder pedals last July I had already been due for a complete reinstall, and I didn't want to spend time troubleshooting what I considered a minor problem. I finally reinstalled everything a month ago. That fixed my problem.
Incidently, that also fixed my problem with the "mouse" button, which had stopped working a few months ago. Now everything works fine, and I'm still quite happy with my HOTAS.
FunkedUp's suggestion should work. Use the NukeUSB and RemoveJoy utilities on the Saitek installation CD (they're not available on Saitek's web site) after you unplugged the USB controllers and removed them from the Device Manager (or whatever the English name is for that tab in the System control panel). Make sure you go to
Ron Hunt's Saitek Help web site and read the section about re-installing everything. He explains the use of NukeUSB and RemoveJoy.
Do as FunkedUp suggests. Install the Saitek combo first, shut down, restart, then install the CH Pro Pedals. Shut down. Restart.
That's what I did last time, and now my Saitek combo is on ID#1 and my pedals on ID#2.
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DrSoya
308 (Polish) Squadron "City of Cracow" RAF
Part of the
Northolt Wing (First Polish Fighter Wing)