i cant disconnect my controller easily, otherwise i would give it a go.
My pumps which were shurflo, have always done this, just flashed de, the contollers are designed that you dont need the pressure switch, and with out a pressure switch, the controller will never flash ps, because there isnt one to cut in.
There is no problem with your controller, that is just how they work, i cant see that the pumps are going to use much power when they cut in for a second when the de has cut in.
Are they actually running your batterys flat then?
Having your pump running on full power without the controller is going to drain the battery quicker than having a flow controller and having the pump cut every few seconds when the de has cut in.