Your description isn't 100% clear. I'm not sure you've gapped both rails of both ends of your reversing section,. That is essential, so if you haven't done so, it is the first step toward a solution..
The only way the reversing track polarity/phase can match the main line at both ends (first at one end, then at the other, not simultaneously) is for both rails in the reversing section (it can be more than one block) to be switched.
If both ends aren't isolated, then for one polarity/phase, the reverser will connect a short directly across the rails. But, it should sense that, and switch back, and the only time you'll be aware of the problem is when a loco crosses the gapped end of the reversing track.
If you have a constant short, then you have a different cause than I described. Perhaps you can send more information to the group.
