Does anyone know what these black spots mean?

Some of the ceilings only show up partially:

and others don't show up at all:


The ceilings on the 1st and 2nd floors render fine but the 3rd and 4th floor only show about 50% of the ceilings. I've played around with this by deleting the windows and replacing them and even that's iffy. It seems like as soon I can get one room to fix, another will start doing it (usually if i make a big change or reinstall the house).

I'm no expert but you may be referring to the game's attempt at shadowing. Of course if you have a dark ceilings you're less likely to see it. I believe it is affected by window and light placements and you may have to toy with it a little.