I am posting here, more to reap the benefit of your experience and obtain confirmation of my recent observations about my particular setup.
Firstly, FSUIPC has been a great purchase. It has allayed much of my previous anxt with joystick calibration and has proven to be a better solution for FS9 than the M$ default system. However, (and I doubt it has anything to do with FS9 OR FSUIPC) often when I would re-open FS9 for a flight, I'd notice that the calibration was completely lost, the rudder (twist handle) would only register to the left, the elevator would deflect only marginally and it would 'spike' like blazes. So, back into the calibration menu for another attempt to have everything work. The device is usb connected to an Asus P4P 800E Deluxe Mb and after many years of investigating this calibration problem, I believe I've found a solution which may be of benefit to others.
Once I have all the calibrations set on each axis, I have my flight. At the end of the flight, ie parked, and with FS9 still running, I unplug the joystick from the usb port. Then and only then, I will shut down the program. When I re-boot the program, I set-up my flight (this can take some time as most of the aircraft I fly are payware), thence to pre-flight walkaround and reconnecting the joystick. Lo and behold! Everything works!
Pete, have you ever experienced this? Could it be a shortcoming of the Mb or summat? It has taken me years to find this solution (which works for me and I hope, other people having the same frustration). My joystick is far happier lately, too and my hat is off to the manufacturer for producing such a robust device.
Jon