ill have a look.
i cant replicate the problem, in cli mode, i doesnt work at all, in flight mode it worked fine.
Step by step here we go:
Connect via Xbee, do throttle calibration in flight mode through setup radio in the gui.
Disconnect Xbee, connect USB cable to Ardumega after selecting terminal on the selector switch. Type Setup. Receive message, your Radio has not been calibrated or setup please run radio. Not word for word but you get the idea.