Its got nothing to do with pilot input.
Essentially, hydraulic pressure is removed from them during takeoff which causes them to droop - then lift aerodynamically with increased airspeed. Then at x kts hydraulic pressure is restored and they return to the commanded position. I don't think its covered in the FCOM etc but I believe its to do with preventing unnecessary stress on the flaperon actuators.
Cruise flaps; black box technology as far as pilot manuals are concerned. It just works!