I don't think that the longer power stroke is the reason for short brace height bows being less forgiving. As Frank mentioned I had actual #'s to back this up a while back, but am unable to locate them now. The shorter brace height bow does have a longer power stroke, but because they are usually on bows with faster cams, the amount of time that the arrow spends on the string is actaully less. I think the reason that shorter brace height bows are trickier to shoot is that with highly reflexed riser designs (i.e. limb pockets way in front of the grip) they are very torquey and magnify small form errors.

Personally another reason I have trouble shooting some short brace height bows is because they usually utilize radical cams which come with a significant exposion on release. I would anticipate this and flinch upon release after a few rounds of shooting and my groups would open up. So it's not an inherent fault of the bow having a short brace height, but my inability as an archer to have perfect form and release.