400,
You should not need to initially open up any of the valves...
In the Pool mode, the automated Intake valve should suck all of its water from the Pool, and none from the Spa.
So, if your spa drains down with the pump running, water can only get out via the Spa drain.
In theory, your Intake valve is leaking, or the actuator is not moving it to the fully closed position, and allowing water to be sucked out of the spa drain.
Since this has been going on forever, how about showing us several pics of your equipment pad.. Maybe we can spot something. Make sure you show us the automated Intake valve, so that we can see where it is position in the Pool mode.
Thanks,
Jim R.