The internal bypass in your heater is probably setup to make sure youre always getting about 50 GPM through the heat exchanger and sending the rest past. Auto-Pilot's bypass system for their SWG works in a similar fashion. Also, This bypass probably has some type of check valve, and you probably have another one between the heater and your chlorinator, and I'm guessing that you are hearing these valves when they slam shut. If you take a spare Jandy Check valve and manually open it and then just let go it pops closed with a very audible thud.

Brad
Waterworks Pools