Waypoints and unit locations are altered randomly from their position set by the editor. This results in indeterminate behavior, exemplified by the two versions of a mission attached below. The elements were copied from one mission and pasted into a new mission in the editor, and positioned as a group in almost the original position. Upon loading the two missions, however, the helicopter is in dramatically different locations. Further, when the Alpha 1-1 unit travels to its first waypoint, waits for the helicopter to land, then boards the helicopter, the helicopter will immediately take off in one version, but stay put in the other version (I believe this has to do with the distance between the helipad and the helicopters next waypoint, which is increased beyond a certain threshold by the random variation.)
While having random variation in unit initial position and waypoint position can be an excellent way to spice things up and make the game less predictable, it can, as in this case, royally screw with the mission. I propose making this an optional setting for placed objects, i.e., click a check box for the unit or waypoint to be affected by randomness.