If any group is given a waypoint and has a vehicle in either "Wheeled_APC_F" or "Tank_F", they will not complete their waypoint. The vehicle has been assigned to the group using (group) addVehicle (vehicle). They will enter the vehicle appropriately, but they will never move to the waypoint. Any vehicle of any other class will work just fine.
One work around is to wait until after the units have entered the vehicle. Then change their group (steps below) and reassign the waypoint. They will behave as normal.
Note, this is not due to the commander position, as not all of the vehicles in those classes have a commander position. I first noticed this after the Tanks update.