I have a Cougar and I don't have a problem with calibration. Here are a few things to try.
Use the latest firmware and you can find it
here . There should be a new version coming out any time now and I hope to see a fix for the manual calibration.
I use Auto-Calibration with the current firmware because there are problems with the manual calibration. Use the Launcher every time you start AH. Move all your axises to their full range before you start flying. This procedure has worked well for me. I use the Launcher because I have a complex program and strange things may happen if the program isn't initialized when I start the game.
Did you write the AH program for your Cougar? If you use one someone else wrote, there may be things in there that could be causing the calibration to change. As an example, if you are using mine (
Gunner's Cougar Page ), there are several things that change the profile and calibration. I use the Cougar Trim, and if you hit that by mistake, or forget to turn it off, it will be out of calibration. If you use my undocumented bomber calibration, it needs to be turned off before returning to flying. The axis profile also changes depending on the setting of the Dog Fight switch.
Also check to see if the program isn't using a profile that uses a manual calibration or strange axis profiles.
If you don't think any of these are the problem, when strange things are happening.... flash the stick and do a good initial calibration. This is easy, just run the "Flash Upgrade" from Foxy and follow the instructions.
Good luck.
Gunner