Thank you for all the responses, I'm still looking into this and trying several things.
My wife and I did try to use the spa yesterday and when we turned the control panel inside the house to "spa mode" it started slowly draining the spa into the pool. I have attached a picture of the equipment pad and labeled the water flow as best I could. The spa is elevated above the pool with a spillover into the pool.
When I change the mode the pool is in, the 2 Jandy actuators change the flow of water from and into the pool/spa.
Pool Mode - Water is taken from main drain and skimmers and flows into the pool and spa.
Spa Mode - Water is taken from the spa drains and flows into the pool & spa.
In Spa Mode the actuator on the valve that feeds the return jets isn't completely moving over to the spa only and it's putting water back into the pool & spa.
Is this normal operation?! Shouldn't the water be pulled from the spa drains and then put back into the spa only? In this picture the handles seem to indicate that the water is coming from the pool drains and skimmers and flowing out through the right side return with the check valve on it. That should be to the pool because the pool jets are working right now yet the spa's spillover is also working

.
In Pool Mode the actuator on the valve that feeds the return jets seems to only point to the pool yet there's water going into the spa and the spillover is working.
Also in spa mode (no blower on) the pump's filter basket is full of air bubbles, so I think there may be a leak somewhere between the spa drains and the pump because it doesn't pull in air otherwise.
I'm very confused, we've used the spa before and didn't seem to have these problems like we are now; however, power outages that happen in my area seem to play heck with the aqualink system. Any and all advice would be appreciated. I really need to know what these valve positions *should* be for normal operation and if they are off in some way!
Thanks everyone!