When a window is has a transparent background then it will not be rendered correctly and will be rendered black instead.
In the example attached, there are two approaches to reproducing this, one is to set a transparent background on a Window that is shown above the other. This will show the problem some of the time, but not every time and can be worked around by using:
The other approach which is commented out in the first Window is to change the background color from transparent to a solid white, this will then cause the second Window to have black instead of transparent pixels then.
Update: The workaround will cause other problems when on macOS 10.13 and having text that has an alpha channel, so depending on the setup, the workaround may or may not be viable.