I have a CH setup also, but I have never used CH Manager. AH has always been CH friendly and one less program between my controllers and the game can't hurt.

After mapping secondary select as BACKSPACE, everything worked the same in an aircraft.
I think the confusing part is that it is not explained that we must now change "modes" (use a different stick set) when in a gv or a bomber. We didn't have to do that before, since FLAPS_UP and FLAPS_DOWN (keyboard Q and W) for aircraft automatically worked for changing gears in a gv, since they are the same keyboard commands.
Why the same keyboard command doesn't work without changing to another "Mode" or stick set is still a mystery to me. I don't see how a different stick manufacturer would make any difference since Q is Q and W is W if mapped to the stick.
There must be some reason though, and we all just don't know the reason.
The trigger for the stick function was in the type of vehicle (meaning fighter/attack/, or gv or in a bomber) before, I believe.
Anyway, If I could figure out the naming system for the .jsm file in the settings folder, I thought about writing a simple, clear, step-by-step utility that would save the files and bypass the in-game function. I still don't think the in-game GUI is very clearly written.
I think all of us are guilty sometimes of assuming the average new person "gets" what we usually needed help to set up ouselves years ago.