Does the chopper have a waypoint that is syncrinized with one of the unit's waypoints? If so, a script that alters the unit's waypoints will tend to mess with any other unit (like a chopper) that has any waypoint synced with the unit in question. Try using a script to control the chopper rather than traditional waypoints. you can put invisible "H"s for instance and make a "Unit domove" script to make the chopper move from one invis. "H" to the next. You will have to name each invis"H" and if the chopper needs to land at one of the "H"s to pick up the unit, you will have to use a script for that also. For the most part, I have found scripted movement to be more reliable and ADJUSTABLE when it comes to syncrinization beteen units, than the standard editor waypoint placement.