Not sure why it does what it does but my recommendation would be to do away with the bypass, reroute the plumbing with your flowmeter on the output of the pump to the section valves and run the pump with a PWM valve, I have done quite a few systems like this and they work very well, Unless there is a reason there is a reason you need a bypass that you didn't state. Personally I have never seen a bypass system work all that well.