Let me put it another way, I have been a pool & spa repair tech in Phoenix,AZ. for 25 long years, I have worked on thousands of pools.
First off, even the spa jets if the 3-way auto return valve was set to spa "on" and the 3-way auto suction valve was set to spa "off" would become pool returns.
When you describe this fountain thing, do you mean on of those cheap ones that float on top of the water and connect to a return line for there water pressure?
It sounds like you have one of those connected to the spa return line that is used to provide the water to go over the spillway back to the pool, when your in normal filtration mode when you don't use the spa this is how it run's
Your not supposed to turn off the return from the spa that goes back to the pool, which in this case would be the fountain as you describe it, all spillway spas when spa is not being used operate this way, they have a return "on" with the spa suction "off"
When you turned off the only return the spa had in the fountain, you in effect shut off any circulated water back to the spa "you isolated the pool from the spa" that means the spa would just be another big glass of non moving water, that you would notice in a few weeks would be green, and the pool blue.
There should have not been any water loss occurring in the spa other than evaporation if it sat for two weeks because the suction and return were both off.
The fact you shut the only return the spa had back to the pool when you turned the fountain off, and that the water level only drops with the pool "on" and does it that quickly, tells me instinctively that it means the spa suction is open slightly, because if the only return was turned off, and the pump turns on, and the spa starts getting lower water level, means the spa is being drained into the pool, which you couldn't see when the fountain was on because the fountain was returning more water to the spa than the spa suction was taking out.
Does this make a little more sense now?
The fact that the valves are "automatic" has nothing to do with anything, and looking at the valve and saying it "looks like it's closed the best that i can tell" is not the same as looking at the valve and saying "i checked it all out, and without a doubt that valve is closed"
Good luck, try to wrap your head around my logic here, i think it will make sense to you. (the pic is one of my residential service accounts, be glad you don't have to deal with that)