Phil,
I can't tell for sure how your system is wired, because all the wires blend together in the pic..
But if you look at the label on the SWCG transformer, or just look in the manual, it makes it pretty clear that the SWCG transformer should get its power from the load side of the Pump/Filter relay. The Pump/Filter relay only closes when the system is in the Pool or Spa modes AND when the pump is being told to run.. In the old days, the Pump/Filter relay used to provide power to a single speed pump.. But, the IntelliFlo VS pumps are connected to constant AC power so they do not use a relay.. The Pump/Filter relay still acts like it is controlling the pump, but it now only controls the SWCG transformer.
Look at your system and tell me where your SWCG transformer is getting its power.. If not from the load side of the pump/filter relay, then it is just not wired correctly or safely..
The cell does have a flow switch, but this switch has nothing to do with electrical power.. It is a back up safety device that prevents the cell from working, but will not turn off any power. It basically controls the flow light on the cell... Green = good flow and Red = low flow..
Thanks,
Jim R.