In approaching this problem, it must be remembered that the centrifugal pump is a slave to the system, so when there is a difference in pump output, there must be a difference in the system to require that change.

With a discharge pressure reduction from Pump B to Pump A, (and assuming these pumps are identical!) there must be a difference in the total head required by Pump A. Such differences can only come from the system. As you indicate there is a difference in the suction side of the two pumps, then it would be logical to assume that the difference is the source of the problem.

Hope that helps.