Isometric tiles are not drawn transparently, if they contain parts that should be transparent. To reproduce:

1. Create an isometric board in the editor.
2. Lay some tiles (.tst or .iso) on layer 1.
3. Lay tiles with transparent sections on layer 2, over the tiles on layer 1. Parts of the tiles on layer 1 will still be visible in the board editor.
4. Test run the board. The transparent parts of the tiles on layer 2 are rendered opaquely and the tiles on layer 1 cannot be seen.