Flap operation

Hello All, this is my first post to this forum so I apologize for all of my newbie errors.

The "executive summary" of my problem is: I cannot reverse my flap output channel.  When I change the CH5_REV from 1 to -1, the flaps physically move from fully down to up then go back down all within one second.  Changing from -1 to 1 has exactly the same effect (flaps go up, then immediately return back down).  Changing the RC5_TRIM from 1000 to 2000 has no effect (which does not surprise me, but the down-up-down sequence does mystify me).

I am flying a Pixhawk in a plane with separate ailerons and flaps.  The flaps are retracted (fully up) when the servos receive a 2 mS pulse ("2000") and fully down when the servos get a 1 mS pulse ("1000").  FLAP_1_SPEED,  FLAP_2_SPEED,  FLAP_1_PERCNT,  FLAP_2_PERCNT, FLAPERON_OUTPUT = 0.  I am using a 72 MHz RC radio and a PPM encoder.  When the RC transmitter is switched off, the encoder outputs all channels 1.5 mS and 1.0 mS on the flaps channel.  Channel 5 output is 1000 because the Pixhawk will output the larger of two inputs to the flaps and I want to use the flaps in auto takeoff and auto land mode.  (Pixhawk docs - "If you have both a FLAP_IN_CHANNEL set and a Flap_auto output function set then the amount of flap applied is the higher of the two.").  If my encoder outputs 2000 to the flaps, then the flaps will not be deployed in auto land or auto takeoff modes.

So! my questions are:

1) why do the flaps go down-up-down instead of reversing with CH5_REV is changed from 1 to -1?

2) is there anything short of physically flipping the servos over is the wing that can make the channel 5 reverse?

Thanks!

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