I have been running into weird problems when working with tile layers with alpha transparency. The bottom layer, layer 0, is a solid color with no transparency. Layer 1 has semi-transparent tiles which do not show correctly. There is a display issue where it blacks out tiles that should be transparent. There are other weird behaviors if you put a single lighter colored tile in the darkened area. This is in the most recent beta version, listed as 6.011.
This is the way the level should appear, and appears in the Gonstruct editor:
This is how the level appears in-game:
Opening the .nw level file shows that the tiles are where they should be, and if I create an NPC to tell me which tiles I am mousing over, it even says the correct tile index. It looks like it is simply some sort of display bug unless I am missing something.
Here is the level and tile set I used:
tilelayeralphabug.nw