Description
The part of the building that is gone here has a content error where it was assigned to a transparency layer despite being a solid mesh with depth writing enabled. The problem is, whether it'll appear above or below the clouds is entirely dependent on the loading order. Loading order is basically a race involving the background threads and seeing who finishes first.
The issue doesn't usually happen in original hardware, and it also doesn't happen to me personally on Linux but it does happen with the very same hardware on Windows, hinting that the problem can be related to the CPU scheduler behavior of the OS and multiple other factors.
The easiest way to make this not dependent on the hardware or the system would be to patch the content error specifically for this model if the geometry is unmodified.