OK i don't know what was wrong with it but I used "set to face" and it fixed it.

Now i'm having more issues with the same face. I've got the windows and now i want to draw a horizontal edge at the base of each window for a window sill (that spans across the walls as well).

So i used the split polygon tool to draw more edges, turn snap to curve on. and i can draw the line ok, but when i press enter it covers up some windows. (i.e. the window indent is still there, it's just covered up by a face in front of it).

I don't understand where this face comes from when i only add an edge.

I've added a pic of the problem. THe orange edge is the one i've just added, and it's caused two windows to be "covered".

EDIT: ok i've played around some more, and the same thing happens if i cut the face in half. i'm guessing when i split polygon i'm doing the same thing.