I once had a similar issue. I was purging the water lines with fresh water, then left the pump on to see if there were any leaks. The pump cycled every one or two minutes. I had not yet filled the water heater and was flushing the system in by-pass mode. I was unable to find any leaks anywhere. I filled the water heater with water and then left the pump on and the pump cycling stopped. I never did find a leak anywhere and have concluded that the by-pass valve must have been leaking very slowly into the empty water heater. Once filled, problem gone. I sincerely hope your issue is resolved as easily and cheaply as mine. Hope this helps.