I have never seen anything like this. Interesting but I have no idea.
You can test what your Org files look like by launching Emacs with emacs -q (in your terminal, or on Windows, in Start menu). This way, you don’t load any of your configuration. My guess is you don’t have the same problem if you don’t load your configuration.
If so, it will be a matter of finding which package / part of configuration is causing this problem.
It’s possible nano-theme is doing something. Do you know how to disable it to test the idea?