~S~
I get occasional wierdness too - I use my venerable old sidewinder precision pro in combination with the throttle half of an X-45 set up (the stick sits under my desk in disgrace, I don't like it at all, and I need to use my sidewinder because the x-45 rudder on the throttle unit is unusable)
Sometimes in the past I have lost either aileron or elevator control on the stick at odd times. Apparently this is due to some other HID device or driver kicking in and confusing things - that's about as technical I get with regard hardware...

- thanks to the guy on ebay who helped me with that!
Anyway, I seem to have solved the problem (I hope) by turning off some of the settings under Control Panel > System > Device Manager
I turned off the Saitek Magic Keyboard and Magic Mouse settings under Human Interface Devices. I think this means that I can't program the saitek part of my set up to do anything more than I can assign in game, but that's all I really did anyway.
Hope this gives you a head start at least,
Cheers,
Pads
http://www.caw15.com