Higher elevation Jacuzzi backflow issues

[lordofcatan]

Hello, thank you for having me here. I recently bought a house which has a nice lap pool along with a jacuzzi which is at a higher elevation than the pool. About once a week I have to put my AquaLink into "Fill spa" mode to pump water which was "lost" into the pool due to gravity back up. What I gathered so far is that this happens when the daily schedule for "spa" mode kicks in. I have installed two additional check valves on both intake sides (see diagram) and I think I can clearly see what is happening. The second the spa program kicks in, the pump goes off. The Jandy intake actuator is still drawing from the pool and as it turns the diverter, both check valves are open, allowing water from the higher elevation jacuzzi to flow back into the pool. My questions are:
1) Does the theory even make sense?
2) Is there a way to build in a start delay for the pump? The thought is to have the actuators finish their job before opening the pump. According to my readings of the AquaLink there isn't, but who knows.
3) Can you configure the AquaLink to have the valves in "spa" mode be the "default" position?
4) Any other suggestions to address this?

One last thing, I know I have a make-up valve, which might be able to do the trick, but given that my jacuzzi would overflow onto the pool's cover, I would rather not refill the jacuzzi every time the pump runs.

Here is essentially the plumbing and my equipment should be in the signature.