With that pump/res setup I doubt it's air as the air would go straight up to the res when you shutdown. I would manually inspect the pump and make sure there's no gunk that might be holding it back. You make it sound like the RPM reading is accurate and that the pump is not moving when this happens, so I wouldn't unplug the rpm connector as it's telling you useful information. It could be that the pump has a sketchy electrical connection - try wiggling the cables to see if that causes it to start/stop. The connection could be weak in the molex connector of the pump, or at the solder joint to the pump body or in the psu cable itself. Try swapping the PSU cable to be sure it's not that.