Have you mapped the throttle to the correct game throttle? I think there are 4 seperate throttles in the game - one for each of the multi-engined aircraft. Cant remember which one is the default one (which controls all engines at once).
The setup has all changed recently and im no longer familiar with it, but maybe this somewhere to start?
btw - i got pro CH USB gear, and i dont use the CH software at all. Just plug em in, calib in windows, calib in AH, then set your mappings up in AH, and your away.