Isn't the Navi board responsible for AH functions? Is MKTool telling you anything? Seems you should be able to get a GPS fix inside, and just raise and lower the copter by 1 meter or 2 and watch the readings on both MK boards. And did you do the little velcro mod that Andy recommends in his video? He strongly suggests covering the air pressure sensor on the FC with some velcro (or something similar) so that it is less susceptible to windy conditions. Worth looking it, although you probably know about that already.