The first thing that comes to mind is the error with layers. Ie the floor is placed on Floors Overlay 3 or higher. But if you say that he is from the BMP, then most likely that is not the case. Maybe in Rules.txt you need to specify on which layer it will be displayed. I have not tried to do this, but it seems there was a similar position with plants.
Second idea - did you forget to register in Tile Zed - Tools - Tile Preporites for this floor tile that it is floor (IsFloor)?
Third - if you add vanilla tilesheet to your texture pack, then it will automatically make a second file "your_texture.pack" and "floors.your_texture.pack". The second file will have all the tilesheet named "floor_***.png". Maybe the answer is somewhere here.