Yes that's exactly what I experience, I use the keyboard for rudder, but it sucks, I'm so used to the stick in the other games so my flying skills are limited in WCP.I'm glad I'm not the only one with this issue . I still say a dll hook would be the way to fix this.
For those that may have forgot. The joystick z axis defaults to reverse of what it should be on every joystick i have ever tried. If I go to the options and click "reverse joystick" it will work correctly until I hit the shift key or pull the second joystick button, then it goes back to being reversed. I think most of us just disable rudder on the joystick and use the keyboard for rudder. But still it would be nice to fix