They don't call them "LogiCRAP" for nothing!
OK start from the beginning. Go to the game controllers section in windows and check the stick there. Right click on the stick and select properties and see if the stick responds correctly. Move it through all axises and watch to see if it moves to all 4 corners of the box. If it is all messed up here it is most likely a problem with the stick. You could delete the controllers reboot and try re-installing it to see if that clears it up.
If it works fine in the windows test then it isn't being recognized by the game right. Going through the complete setup.... use the drop down to select the controller, high light the controller and select advanced, calibrate all axises, select each axis for each control elevators, rudder and so on, and save it.
My guess is the stick is more than a year old and is failing. Good luck!
