If I understand your question, you are asking why the windings in your motor are running hotter when you increase bypass flow. If I have interpreted this correctly, then the answer in easy. When you open the bypass, the total flow produced by the pump increases even if the flow going to the boiler may decrease. If the total flow increases, then the pump is doing more work. More work requires more motor horsepower. If the horsepower goes up, then the motor may run a little bit hotter. Please correct me if I have misunderstood your situation.
I am confused by the last part of your post. You say that the bypass opens when the discharge pressure is low. Normally, I would expect the bypass to open when the discharge pressure is high; indicating a low net flow from the pump. If the discharge pressure is low, this would suggest higher flow from a centrifugal pump and no need for minimum flow bypass. We need more details to understand what you are describing.
Johnny Pellin