I'm not experienced with pumps... but here's my best educated guess.
Usually, these things are designed to start pumping when the pressure reaches some low threashold, and keeps pumping until the pressure exceeds a higher threashold.
I'm guessing that when only one circuit is on, the pump is able to quickly go from the low pressure threashold to the upper threashold. Then as the pump loses pressure, it quickly drops from the high threshold to the mid-point, but takes longer to drop from the mid-point to the lower threashold. As a result, the average pressure/flow is on the low end between the two threasholds.
But when you run two circuits at the same time, the pump can bearly keep up, and is nearly constantly pumping. When it does reach the high threashold, it rapidly losses pressure (because it's running two circuit, and quickly resumes pumping. As a result, the average pressure/flow in on the high end between the two threasholds.
If I'm right, and if you can adjusts the high/low pressure thresholds (that makes for a big if) try adjusting both threasholds up and run just a single circuit and see if that does better.
What I do recall reading about pumps is that you want them sized/set such that they don't cycle on/off very frequently. That just causes them to wear out faster. Instead, you want them sized/set so that the pump stays on most of the time and doesn't cycle very frequently. It's sort of like you get less wear on a car engine if you constantly drive at 70mph than it is if you speed up to 30mph, then slow to a stop, then speed up to 30mph, and slow to a stop.