In a parallel pumping system employing centrifugal pumps, suction and discharge pressure loss due to piping and fittings is the cause of significant flow variations in cases when the pump curve (Head-Flow) has a steep decrease of head with increasing flow. A small change in the head requirements causes relatively big change in developed flow of the pump.
Imagine that pump "A" has more pressure/head loss in the suction piping, than the pump "B". This results in lower NPSHA and lower suction pressure of the pump "A". For constant discharge pressure for both pumps, the pump "A" now needs to develop more Head than the pump "B". To develop more Head, the pump operating point has to shift towards left side of the curve, towards higher Head. If the Head-Flow pump curve is relatively steep, shifting towards higher Head means significant decrease of flow developed by the pump. This could be your case, although we don't know the pump details.
I suggest you a good reading - articles from Joe Evans available at Pumped 101:
http://www.pumped101...llel part 1.pdf
http://www.pumped101...llel part 2.pdf