3D Window Transparency settings used to affect the display of windows in the schedule, but I think that's no longer the case.
Have you been playing with your fill types in this project by any chance? In particular has the Air Space fill been replaced by a Solid/Foreground/Background/100% Fill?
Maybe try starting a new project from the defaults and test the appearance there to see if you're getting the same issue?
Cheers,
Link.