Tiles will do that if the parts of the tile model do not follow the correct naming convention. For tiles where it matters which direction the tile floor is rotated in, the parts of the model that make up the floor should have the _RF suffix (Rotatable Floor...). For tiles where it doesn't matter if the floor is rotated with the tile (flat floor with one wall for instance), only _F is necessary. The _F or _RF identify the model piece as a floor for purposes of determining the floor texturing the tileset. Technically you'd want _RF for all your floor pieces as good practice, but with seamless textures it's not visually needed. A number of tilesets suffer from that bug, including the stock Shadow Fortress tileset.
I tried to correct the model part naming bug in every tile I found it in, are you using my tile pack?