[f5soh]

Some Atom boards have issues with PPM on pin8 (bad reverse-engineered) , if you use PPM you may try PPM on flexiPort.
https://librepilot.atlassian.net/wiki/display/LPDOC/CC+Hardware+Configuration#CCHardwareConfiguration-MainPortandFlexiPortserialcablepinout

Take a look here:
https://librepilot.atlassian.net/wiki/display/LPDOC/RC+Transmitter+Wizard#RCTransmitterWizard-FrequentlyAskedQuestions

Edit: Sorry, you are using PWM input
How about the receiver activity ?
Whatever the mode 1 or mode 4, that the first step.
https://forum.librepilot.org/index.php?topic=2517.msg17775#msg17775