This is something that has started with my move to the newer Xcode and some updates to wxWidgets. Haven't figured out what's going on yet. Might be a compiler bug, wxWidgets bug, don't know. When running on Mojave, the issue doesn't appear and it properly flips back and forth between light/dark mode. On older OSX, it SOMETIMES (not always) gets the black color.
You can go to Settings->Color Manager and set a different color for those. That said, once you do that, when Mojave is released and you update, it will stay at that color instead of flip to the dynamic color.