http://www.filelodge.com/files/room19/510903/ex.bmp

This is a problem which I can't fix. The empty tile in the left above corner is working fine, but other tiles which are suposed to be transparant, aren't. Does somebody know how to fix this?

I'm assuming at this point you aren't using "Remap tile set palette" and your set has a working palette. If so, the solution is relatively simple. Just make the color you want to be transparent the second entry in the palette, and make sure the first entry is #000000.