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.