These units "portDefense.mis" are place in the game by Random Gen Groups and use waypoints to travel around the game world (looped back to first point).
I think this issue is not just in scapa, but most ports where there is land and shallow water.
DDs that never stop (deep sea) are from convoys and are place in the game by generators and use the common paths set by nodes to travel around the game world (a to b).
Could it be this method of generation and waypoints that is causing the problem
Edit - no it can't be as this is also the method used in single missions and they work ok