Interesting you should ask, this question has just been answered in the Bluecoat internet forum. Unfortunately I deleted most of the postings, but this is what I can remember.
Due to the characteristics of air (compression, behaviour as a fluid, etc) the flight envelope with flaps extended is only tested in those regions where flap extension is likely to happen (ie below 20,000'). Above this level the characteristics of air are such that it could cause changes the behaviour of the aircraft. Someone was saying the extension of flaps at high altitude could have a negative effect on maintain control of the aircraft. (Leading edge devices are said to be inhibited for the same reason above 20,000'.)