Looking at the log its not seeing ANY RC_IN at all. Its like the Receiver isn't connected. I don't know of any setting that could prevent RC_IN. So either your BBB is having a problem or your receiver is having an issue.
Hmmm, you do have ARMING_CHECK at 0 but ARMING_REQUIRE is 1. That's an odd combination. You saying don't check anything but don't arm unless the checks pass. I still don't think this will affect your RC_IN but I'd change it and test again just in case.