As far as the one i have on, I keep it up almost all the time. My wife is a very white-skinned red-head, with family history of skin cancer, so we keep her covered as much as possible. I have had no problems at full speed with it up.
I tend to catch air if I have it up with only me in the boat. I can hit a small wake and the boat will come out of the water for a little ways. I think some part of this is due to the top being up and sorta acting like a wing.
It does not flap or move at all. Sometimes the front straps will vibrate, but that is about it.
I noticed that the wife accidentally put her side strap on with a half twist last weekend, and it didn't vibrate at all on her side.