All black colors become transparent

If your color 0 (the transparent color by default) is also set to black, then, after removing unused colors with the Blacken function, a tile map project decides all black colors are transparent from that point on.

The workaround is to set color 0 to something else, such as magenta. This makes the program realize that black is, in fact, a valid color and render the rest of the palette appropriately.

Thank you for the report. This bug is already fixed with the upcoming release.