Can confirm themes are responsible for breaking the check marks on the options boxes in big box mode, I had the problem during the beta (was only in it for 2 day) and thought I'd leave it be and muck about with the program once 5.0 launched, I just found this thread and I was using a custom theme with the same problem reverted to one of the standards and it fixed it, not ideal since I prefer a darker colour but I can always switch back once I've finished with the settings.
In case this info is useful to you I'm running windows 10 nothing particularly odd about my setup and toggling the theme back and forth makes the check marks appear and disappear so it's definitely that.