Auger,
strange - I've been using CH Stick&Throttle for ~ 6 weeks - NP. Last saturday I installed my new CH pedals. Went into game offline and had lost all the stick/throttle analog and key mappings!
Remapped the stick, throttle and pedal/brake, flew a bit offline and shut everything down. Restarted the computer and windows tells me it found new hardware - reinstalled all and back in game - poof - everything gone!
Remapped again - shutting down completely several times - no further windows new hardware notifications and finally got CH configured in game. Sunday, went online (after flying offline for ~ 20 min), spawned a plane and in air had no controls (auto takeoff). Checked controllers and nothing was there! Didn't get any ding sound (at least that I heard).
Remapped online (getting better at remembering what keys do what) and since then have had no problems (other than flying like a spastic bat - new pedals are tough getting used to).
Don't know if this is the same type difficulty you experienced, but I thought it was strange. Incidentally, I don't use the CHCM, but assign all functions directly to controller in game.
Regards,
Optiker