I did a test build of your arrangement and was able to duplicate what you are seeing. It is an issue that has been around a while and your post has been merged into that thread.
From your pics, I think you are building a castle with a perimeter wall that is on a raised foundation. So to make the invisible parts become visible again, you are going to have to break that wall somewhere. Deleting one tile is enough. So I suggest you pick a spot that you can hide with landscaping or an object so you don't ruin the look of what you are building. Another thing you can do, is to scrape the raised foundation and just use a flat foundation.
Hope this helps.
