I had a Flojet that played up like this on a two man system. Always when the tank got low and water was sloshing about. It let air in the system. It was a right pain to get the air out even running the pump flat out. The air would come out but the controller would never dead end properly. The other side of the system was fine. It was always this one side that played up. We tried a different controller, connectors, everything we could think of. I emailed Ian Sheppard several times who was helpful. Turned out to be the pump. I swapped it for an old Shurflo I had lying about and it's been fine ever since. The Flojet always worked but was hard to calibrate the digi controller for some reason. Really weird. I keep it as a backup now for an emergency though with two vans & two man systems in both I doubt I'll ever need it.