After trying many many things, I fixed the level editor's failure to draw identical tiles layered on top of one another. However, it's so hacky and ridiculous that I hate it!
The bug is caused by one of those internal MMF behaviors that programmers have no access to. It seems to be pure luck that it works in KS itself.
When KS draws a screen it adds whole layers at a time. When the level editor draws a screen it goes tile by tile. This is so when you change one tile it only has to update that coordinate's stack of graphics. What difference in these 2 methods causes one to work and not the other I cannot determine.
My solution, is to draw each tile in 2 parts. For each layer I split the tile in a different way. It never draws the same partial tile in the same spot, so it works even when it's the same whole tile.
I haven't released it yet. It should be out soon.