I have a similar problem using the Esky 0905A controller for a helicopter model under Windows Vista. Even though I can see the first 4 chanels working when I calibrate the controller, the throttle control fails to work or is being mapped to the pitch control (assigned to chanel 2) once I return to a simulation.
The chanel 2 pitch control is always reversed too, no matter if the "inv" box is checked or not... The controller is obviously working correctly since everything moves when it is being calibrated, and everything works perfectly - first try with the default setup - under the ClearView simulator.
When I calibrate, I see the chanels working as:
1 = roll
2 = pitch
3 = nick (throttle)
4 = tail
But some (pitch and roll) require the "inv" to be checked, to get the right direction. As mentioned above, checking the "inv" for channel 3 seems to have no effect at all. Once back in the simulator, chanel 3 seems to do the same thing as the pitch control does, and chanel 2 seems to work as I would expect chanel 3 to.
Although I sort of got it working a little bit, none of the controller inputs were close to the way they would be used for real flying, so I finally gave up after trying every thing I could think of for two or three hours, and purchased the ClearView simulator - since it worked perfectly "right out of the box" with this controller under Windows Vista. Now if I could only learn to fly, and have a flight of longer than 15 seconds!
Hopefully a future version of FMS can correct these problems!