Celeborn,
your question has pretty much already been answered. Ill clarify and add a little more info here:
The game interface changed a few patches ago. The controller now has 4 modes which can be selected. Mode1 preset for use with planes. Mode2 is preset for use with boats and vehicles. Mode3 and 4 are customisable. In the "Map Controller" window, make sure you have the right mode selected when mapping (you need at least mode1 and mode2 mapped!). Theres also a box "autoselect mode at start of flight" - checking it will automatically select the right mode upon spawning a plane (mode1) or a GV (mode2). If you want to select the modes manually (or use mode3 and 4), youll need to assign keys for manual mode selection.
Oh, and one more thing that a lot of "old timers" get confused with. The H key now toggles the mouse into "flight control mode" with a stuck cursor. This *also works when youre using a Joystick* - the "cure" is to simply hit H key again. If youre using a stick, you can always simply unmap the H key to avoid the issue.
The Trainer Corps has a new help page:
http://trainers.hitechcreations.com - lots of info on game setup, gameplay and tactics (including controller setup).
Welcome back!
