Mapping and 2D effects strange behavior

I have been working with matrix layouts with non-uniform rows and mapping. I can create a json map file that skips extra pixels. However, when I set up a 2D layout and run 2D effects, they end up looking mirrored. Or is it some sort of wrapping? Sometimes looks like the edge rows are mapped to the center rows?
My map files contain a list of all pixels on a string with the unwanted ones deleted. Interestingly, WLED uses the map and X-Lights data displays as expected.