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I noticed that happening a lot to me...I didn't spend too long doing a semi-scientific study of it (like I did with making basements work), but I think that for whatever reason, the roofs don't like being certain dimensions. Odd ones, perhaps? (Dimensions being the grid width/length of them, of course.)
I came across that while trying to make a building with a bunch of roof-covered porches, and the game whined like crazy to the point that I gave up on it, and built something else.