Sorry to take so long with the response, but I have been away for quite some time.
I'm not sure exactly how you set everything up, but it may need to be reinstalled. If you do don't forget the nuke USB program as explained by Saitek.
I think you have a USB x36 combo and an analog TM set of Pedals. You should have set up the Saitek per the installation instructions.
When you set up the pedals they should not be connected in any way to the Saitek. You should be plugging them into an older style gameport. You need to go into Windows Joystick controlers and set them up as an additional stick with rudders checked. You will have to experiment a little with what type of stick to choose. I no longer use my old analog pedals so it's hard to remember just how I set them up.
You ignore, or just click past, the calibration routine in Windows for the stick portion of the calibration and get to the rudder portion (assuming you checked rudders pedals when choosing a stick). Calibrate the rudders, finish and ignore the warnings that you are not finished. If you test it you should see the rudder slider working correctly.
The make sure you go the Aces High and go into the joystick mapping area. Choose the rudder for the rudder axis only and make sure that all the other axis etc. are mapped to the saitek properly.
Hopefully you have already fixed the problem.
Your post is a good example of why it is better to choose USB devices if you can afford it ( I know yours was a gift). With USB there is hardly anything to do.
Ranger Bob