Haven't had a problem like that exactly. It sounds like you are somehow losing prime on the pump maybe. With the pump being below the waterline, it should pick up again. Check for leaks at each hose connection to the shut off valve and the raw water strainer and then to the pump inlet. If I have recently taken the lid off my strainer to clean the basket, sometimes I don't get it back on tight and it sucks air instead of water. My strainer lid has a cork gasket that I had to replace because I wasn't getting a good seal.
Good luck.