Presumably since 1.76.143187, the following is true:
If a unit is ordered to stop by script (doStop/commandStop), they will return "STOP" as their currentCommand. If you then give a new movement order with doMove/moveTo, the unit will return "MOVE" as a current command. This is the expected behaviour from Arma 2 and 3, just as you can overwrite a player given move command with a scripted movement command.
However, if the player manually orders the units to stop with (x-1-6), the units can no longer be scripted out of their "STOP" state, although you can still move them around as expected. They will be in STOP-stateuntil the player manually orders them to fall back or move somewhere. This seems to be a new issue and causes quite severe problems with scripted AI management.