After the Transmitter Wizard is started, some sticks are not detected.
One primary stick not working
If PWM input: Swap wires and check if the same issue still.
In some cases one channel is wrongly detected as a stick due to a channel with jitter.
Resolve jitter issue or do the channel <> stick function mapping manually, using the Receiver Activity information.
Flight mode - Accessory issue
Be sure your flight mode switch or accessory knob/switch is assigned to one receiver output.
Configure your transmitter according to the manual.
Check the monitor output screen in your transmitter.
Flicker the flight mode switch quickly when asked.