You may have noticed that sometimes transparent tiles appear black in game and
they only seem to appear proper after you switch GTA2 to background and back on.
I believe GTA2 gets confused when the map contains same tile numbers with "flat" and "not-flat".
So open the map with DMA Editor and press CTRL+H.
Replace the the respective tile number with the same number and check the "flat" at the "new" tile number.
Consider to reimport that tile again if you don´t want them all "flat".
Now you should get rid of that bug.