Graphisoft probably won't answer, but one of us will.
😉
The first issue is probably because your Floor Plan Cut Plane (FCPC) is not set to cut through the windows/doors which were set to projected/overhead.
Setting the windows/doors parameter to display as Symbolic is one way to fix that if the FPCP cannot do what you need, or you do not want to use the FPCP. Same with the walls: Symbolic (not available for profiled walls).
The mysterious green must be that you have "Show Minimal Space" checked in the Library panel of the Model View Options ... and your fill and pens settings are set to produce a green box. (The attached screenshot shows the checkbox. The fill/pen shown there are pretty ugly too - I've never used/changed this option.) Just clear the checkmark and re-define your Model View Option.
If this doesn't address what you are seeing, please post a screenshot.
Cheers,
Karl
One of the forum moderators
AC 28 USA and earlier • macOS Sonoma 14.7.1, MacBook Pro M2 Max 12CPU/30GPU cores, 32GB