Had the same problem, waypoints don't seem to register at a certain altitude. I use a trigger to execute the paradrop script. And there too the trigger don't seem to work above a certain altitude. But if you set the X-axis or the Y-axis (don't remember which one, don't have OFP on this PC) of the trigger to the altitude of the chopper the trigger does execute the script. So you can jump from higher altitudes. With waypoints, I think it could be a bug. I start off a chopper at limited speed, with Flyinheight 250, giving it a few waypoints, well, it never gets past the 1st waypoint. It just circles around it. The original game had it and the GOTY v1.90 still has this...