That usually happens if you change the size of the tileset.
I don't know how to fix it in Booster's Lab, but in Cave Editor, one would have to go to "Edit Tile Set", and on the right-hand side, there's a "blank" tileset with numbers and some maroon or blue or grey blocks and stuff. Right-clicking on a tile in the "blank" tileset allows one to set the tile property of the tileset which will be saved as a ".pxa" file with the same name (without the "Prt" prefix) as the tileset, if I remember correctly.