Tony,
What you are describing is a variation of the Pascal Principle - water pressure is equalized on to all surfaces of a closed vessel. Although the water flow in to the reactor is slow, the water pressure will eventually build up if the reactor outlet has flow control.
As for a solution, your trick with only using the inlet valve as the control works. This will prevent excessive pressure from being built up in your reactor since there is no/very low backpressure (or head). The drawback is that it is difficult to control. I wonder if they make a PVC needle valve for this type of application ? You can try moving the outlet valve to the inlet side of the reactor -- sort of a back to back valve configuration.
BTW, this is why most houses use pressure regulators to control water pressure within a house. Valves can control the flow, but it doesn't stop pressure from being built up to dangerous levels when the taps are closed.
Hope that helps.
- Victor.
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