We investigated this scenario and this behavior occurs when changing the theme color variation inside the static constructor of the MainWindow of the application. Unfortunately, the static constructor of the MainWindow is not invoked during design time. You can find some more information about that in the following threads: WPF designer doesn't run window static constructor upon starting up and Why isn't my WPF control's code-behind running at design time?.

As a workaround, a UserControl can be created and placed as the first child of the MainWindow and the color variation change can happen inside the static constructor of the UserControl. You can find a sample project demonstrating this approach attached to this reply. 

Regards,
Vladimir Stoyanov
Progress Telerik