Pixhawk Arms with Mission Planner Not with RC

Trying to get this figured out....if anyone knows the fix it would be appreciated.

ESC's are calibrated and also calibrated with Pixhawk.

RC is calibrated in Mission Planner BUT during the Pre-Arm check I get the message that RC IS NOT CALIBRATED and Pixhawk flashes yellow even though the rc calibration is completed.  To test this I disabled the rc check in the pre-arm sequence.  With that done we pass the pre-arm check and get a green light.  Hurray right?  Almost.  I can arm the quadcopter using Mission Planner, but can not arm with the rc.  However, once the copter is armed in Mission Planner, I can throttle up with the radio.

At this point all flight modes are set to stabilize.

Any ideas as to what is going on?

I should add that if I connect to the Pixhawk via the Terminal in MP and view the settings that the radio calibration settings are saved.

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