I had a similar problem.
Holley tech insisted that the pump be mounted below the bottom of the fuel tank. The pump is a pusher not a puller. When the pump works hard, the thermal overloads in the pump shut it off; that's why you did not hear it running. When the overloads cool, the pump runs again; PITA.
I could not mount my pump any lower, so I switched to Aeromotive and installed a return line.
Check to make sure your tank is vented; if not vented you may get the same symptoms.