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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.

Be sure your Rc transmitter profile do not use mixers, check in output monitor one stick movement give only one output active.

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.