Referring to your colour diagram, I'm assuming you have the AR controlling the thin section of track between the two gaps. The only thing I can see being an issue here is that you could have a train spanning both gaps at the same time, e.g. with something conductive like a loco in the lead and cars with metal wheels or on-board lighting (e.g. passenger cars) at the other end. This would cause the AR to try an correct the polarity at both gaps simultaneously, which is not possible.
Do you have this problem if you just run a solo loco around the loop? If so, perhaps you could make a sketch of your track power wiring, including the AR.