Hello Duncan!
First, be sure that your are using the ConDoc PRO drawing set. ConDoc LT is loaded on a fresh install by default. My guess is this is the issue.
If your windows aren’t showing, you can adjust the height of the section plane. first go to the plan scene that doesn’t look right. choose view > section planes… Move the orange one until it is cutting all of the windows/openings. No need to update any scenes, they remember which section plane is active, doesn’t matter that you moved it.
Any wall that is below an opening will add to the hatch and close up your openings. This is rare because usually models are sliced right at the finished floor, so openings shouldn’t have a wall below. It can happen on exterior doors or multi-level structures. You can drill into this wall, group just the portion that is below the door and add it to the 3d graphic layer. It will no show in plan, but will show in section, elevation, and perspective.