I think the issue here is that what the game considers a roof and what you may see as a roof can be different.
The floor (flat) pieces are not considered roofing, only the roof pieces, the 2 slanted thatched pieces early game.
You cant use a floor tile above as a roof, the game does not recognise this as a roof, only roof pieces.

I had that issue on my first home, was getting wet in my house... turned out the floor pieces didn't count :P