Lee198 said;
me flaps work whilst on the ground, but once I'm airborne it's a very different story!
and
The keyboard commands are in the same boat. Working on the ground, but not up top.
It seems to me that if your joystick or the keyboard cause the flaps to operate normally during preflight runup but not once airborne it couldn't be a controller issue.
I expect you will want to get the stick working eventually after all it cost money. FSX is aggressive about plug and play USB controllers. Once windows recognizes a controller, when FSX starts it will choose an FSX default controller driver for that controller if you havn't installed one. I plugged in a CH flightstick and FSX installed a default FSX driver for it before I installed the CH controller manager. I didn't like the way FSX default handled the controller, (was no hatswitch view slew function).
Uninstalling the Saitek drivers and UNPLUGING the stick would be a good diagnostic, remember to go into control panels and reset inputs & button assignments back to FSX defaults, then try flaps in the air.
If flaps work in the air then I suggest getting the current stick drivers from Saitek's website. A word of advice, be sure FSX is using the newly installed driver, not FSXs default.