In motorcycling this is know as 'headshake' that can cause a 'tankslapper.' (Hit up google for some amazing videos) I've never experienced it either on a motorcycle or bicycle but I can imagine how scary it can be.
From what I can recall, if not caused by mechanical means (loose headset, etc) or weird bike geometry (ruling that out for your Scott), it can be caused by poor weight distribution due to riding position. I've read that unweighting the saddle (not standing up) can remedy the shake, or changing the hand postions. Keeping weight oon the front wheel should help the problem, though. Strange that it ceased when you sat up. I would certainly make SURE your QR is tight on your front wheel, every ride.
Wind as a factor? I guess that's possible. How stiff a wind do you think? Do you have deep aero wheels?