I have no idea how it keeps getting to be the wrong size/position, but if you crop out zone 3 and part of zone 2, it works. I even tried it myself.
Here’s the overlay I used, but Episode will resize it when I post it.
I’ve got to go, all I can say is that if you crop (not resize) to get rid of zone 3, and make sure all of zone 1 stays the same, then put the overlay at 0.0, it’ll sync up correctly.