Hi,
My location, hotkey, theme, options, feature keywords, etc. are all showing as default in the preferences window, but they all work as expected. I select the dark theme, which works, but the next time I open the preferences window, it reports that the light theme is selected (even though the dark theme is being used). It reports that the icon is showing in the menu bar, even though it's not, and so on and so on, for all my preferences. My workflows and license remain.
Here are two emails I posted to Omnigroup's OS X talk mailing list looking for help. It may be related and thus may be useful for you.
What the hell is going on?