I've had this problem before. Start over, but this time do not make a tileset. First, make your picture with GIMP and save it as a 16-color bitmap, then immediately open it up in Cyclone (8BP Mode). Make your tilemap there and you should have no problem opening it up in TMA.
Oh yah, usually 8BP mode would reject having that many tiles, but it worked for me. I just tried it out again and it worked perfectly. PM me if you have any more problems.