1. Reaction among NH3 (weak base) and HNO3(strong acid) results in a solution that is a buffer with its maximum buffer capacity in acidic side of pH range.The buffer capacity is concentration dependant and not symetric around your operating point (pH=6 or pH=7). Therefore it is not a simple control problem; you need a more sophisticated contoller, perhaps adaptive or cascade type.The solution towards the alkaline side from the maximum of the buffer capacity curve you can consider as a mixture of 1:1 (on molar base) NH3NO3 + solution of dissolved NH3 in water.If your controller shifts pH towards alkaline, some of NH3 will leave the solution as a gas. The action is not immediate while contolled by hydrodynamics of the reactor.These effects causes what you call eratic contol action.
A solution to this problem seems to me a precipitation of NH3 in form of some salt and removal from the system.
2.Without a packed bed your scrubber actually works more or less as a homogeniously mixed reactor.In such a reactor there is always a part of not reacted input flow in the outflow.Try to rearange it as a pure counterflow reactor.