Hi Luke,
Obvious things first, is everything else showing that is supposed to be in your elevations? are the right layers on? Are the windows still 3D or have you exploded them or turned off the 3D option? Can you see them when you zoom in and out, as you can see if anything is covering them lika a fill.
Sorry if that is all obvious stuff youv'e looked at. If not exactly what is happening?
Craig