I get the exact same problems. I am using the Gold Edition with Red Hammer. The most annoying part is that the End Mission cheat does not work.
I have managed to get past the crashing helicopter after the cut scene by immediately ascending with the joystick throttle. Of course, I am unable to get to the convoy in time to destroy it. I either get shot down by the vulcan or crash trying to destroy it.
I also intensely dislike any mission that relies on helicopters and airplanes to succeed. I like this game, but vehicles, especially aircraft, handle like crap. I have tried both keyboard+mouse and joystick without much luck.
