Yup, sounds like it. I have to recalibrate my Saitek Cyborg Evo every time I reboot. It's not that bad once you get used to it.
Strange, innit...

...!
I've now got the same joystick, the Saitek Cyborg Evo Force, and every time I start FS9 up I have to operate all the joysticks functions, (X-Y, twist, throttle, etc), through their complete range in the game before attempting to control the aircraft, otherwise the engine runs at full throttle and the plane swerves off the runway....

...!
...like me, it's got little or no memory for what I did before closing down...

...LOL...!
I never had to go through this rigmarole with all my other FF joysticks, MS, Logitech, etc....

...!
It seems to be peculiar to the Saitek joystick...!
Very strange...!
Paul...

...!
Win 8.1 64-bit. DX11. Advent Tower. Intel i7-3770 3.9 GHz 8-core. 8 GB System RAM. AMD Radeon HD 7700 1GB RAM. DVD ROM. 2 Terra Byte SATA Hard Drive. Philips 17" LCD Monitor. Saitek Cyborg X Fly-5 Joystick. ...and a Briggs and Stratton Petrol Lawn Mower.