I seem to be having a similar issue. PPM encoder is functional (5 ch, flashing led speeds up and slows down with throttle). I’m using the 2.0.17 version of APM planner.
Looking at my logs, I have a slightly different error:
ERROR 2015-04-25T14:20:24.951 “isRadioControlActive: Error Channel 1 out of range: rcValue=0.000000”
Any idea what might be happening?