Thanks for reporting. That looks weird as I can’t reproduce it in my environment (Sonoma 14.6.1).
Maybe it’s a Sequoia-specific issue since the app itself does nothing when closing preferences.
Are you on the system light mode on macOS?
Gotcha! The theme changes remote.nativeTheme.themeSource back to the default value when closing a window. It includes the Preferences window, that’s why it happens on the system light mode.
@craftzdog the issue is fixed with the recent update (5.9.0-b1) for me.
When I close the preferences now, the main windows with the acrylic effect stays the same.