Thanks for sharing this issue. Can you confirm whether you're running the latest version of NCrunch? The release of VS2019 required us to fix a number of things in this area, so it's possible we've already solved this problem if you're on an earlier version.
If you are on the latest version, would you mind submitting a bug report after you've tried switching themes? It's possible something in NCrunch has failed to register the change.
Do also let me know if you're running any extensions that might have made any subtle changes to your VS colour configuration.
Note that there are configuration options under the Global/UI category that let you set the colour of your NCrunch windows manually.