This is an obscure one but probably important before 1.0: When the map editor is zoomed out, it samples a subset of the pixels on the tiles for the smaller appearance. It's possible for a non-empty tile to have an empty appearance as a result. This should probably have a more sophisticated sampling algorithm to ensure at least that non-empty tiles always have a non-empty appearance at all zoom levels.

The easiest repro is to draw a 1px square border on the outside edge of an 8x8 tile, draw some on the map, then zoom out to the farthest setting.