I checked and overlapping brushes is not the problem. I have some diagonal windows; I will try removing them in one wing and keeping them in the other to see if that is the problem.
EDIT: It also seems that I have misunderstood the use of hint brushes. After removing them all, the central rooms on the top floor are fixed but the side rooms still look like this.
LCDLC Mapmaking Dept.
Maps finished: Hellhouse, Sorry, Worrior 1-20
Maps modded: CubeOrigin
Maps in release candidate: Blockforts, Cannons 1, Hotzone, Icecastle
Maps in beta: Arctica, Cannons 2, Cerulean-River, Igloo, Skygarden, Spacestation
Maps in alpha: Merlin, Totem