lets try to isolate problem (too much of HOUSE MD last night :) )

Check controls\ buttons\keys \ control surfaces\ flaps
assign default F7 to flap increment and check that REPEAT set to zero.
It'll be good to disable FSUIPC for that test.
If REPEAT set to other than zero position - you can get full flaps instead of one notch.

If you'll have properly working flaps that way, - then we'll search FSUIPC.

P.S. me too using right lever at CH Throttle Quadrant for flaps. But i dont use FSUIPC for controls calibration.