I have run in to the following problem: I am Building my Base on Top of one of the Railjard-"Bunker"-Roofs.
When I "upgrade" the Wooden Wall Frames to Walls/Windows, the Walls Disappear / Turn Invisible upon completaion. Same happens when placing Doorframes. The Walls/Window-/Doorframes are still there (I can walk against them / see/climb throu the Windows) and block the LOS for the Charakter (area behind it turns darker), but are Transparent ingame (I can see throu them). I also can see the "Frame" of the Windowhole.
It is irrellevant how far the Charakter is away (while limited by the Space of the Roof) or ahead/behind. Floor tiles/Fences/Stairs/Funiture are not affected. Same to Wallparts who are placed on the ground or 1 Level hight.
The Wallparts turn visible when the Carakter moves Above/Below the Level where they are placed.