I have a similar set-up, with an Aquapure 1400 and a spa that spills over into the pool. I was running it at 5% Spa and roughly 20% Pool before it got too cold for chlorine production. With the spillover option, you can do a lot of things to keep your chlorine dispersed.
If it were my pool, I'd want to answer these questions to try to figure this out.
1) Confirm that my Jandy actuators are in the correct positions that correspond to "Spa Mode" and "Pool Mode". I would want to eliminate the chance that the previous owner had it set up this way to mask a valve problem.
2) What is the FC level in the spa and the FC level in the pool? They may be different, and that may help explain the flow of chlorinated water to the other body of water.
3) Check all the Scheduled Programs to find out how many hrs/day and days/wk that it runs in "Spa Mode", "Pool Mode", and "Spillover" mode. That profile, along with info from #2 above, should help explain the chlorine level.