I too am new to my pool and spa, but I had set the valves manually with the switches on the back. So when the pump would turn on it would change the location of the valves automatically and it would cause the same problem. Now, I rarely touch the switches on the backs of the valves, and if I do, I make sure I set them back. My pipes are labeled, pool suction, spa suction, pool return, spa return, so I was able to figure out what was going wrong and why the spa was draining below the jets. My spa is about the same level as the pool, so I had the waterfall going the other way!
I am sure an expert will step in and give you a better answer. Can you take a picture of your setup? I can do the same and illustrate what I am talking about.
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