Very odd! Do you mind sharing what MacOS version you are using? We had not seen this before on the Macs in our office, so it's possible we need to test on a specific version.
You need to restart S3D whenever you make a theme change. If you change from light to dark mode within S3D, I believe it already tells you to restart the software. If you change the Mac OS theme externally through System Preferences, you will need to restart S3D yourself before it looks correct.
In short - restart S3D whenever you change the theme and then it will look correct
Version 5.0.1 was released with further improvements for this issue. In the past, you had to restart S3D after you changed the dark mode setting in Mac OS. Now, Version 5.0.1 should detect that changes automatically so that you do not need to restart the software. So the issue that was originally reported should now be resolved.