IN order to get a chopper to fly above 120m, you cannot use standard waypoints. You have to use the "move" command.
The way I do it is to use gamelogics as waypoints and a script like so:
chopper move getpos gl1
@chopper distance gl1 < 700
chopper move getpos gl2
@chopper distance gl2 < 700
This is messy but it works relatively well. The distance ususally has to be adjusted according to the alititude the chopper flies at. I can get choppers to fly at 450m using this method. Any alitiude over that will never work.