Mail Doesn't Store Display/Window Preferences

I tried resetting Mail to its defaults and deleted all the usual suspects, the Preferences plist, the Application Support directory, and the .savedState folder. The .savedState folder was a symbolic link—I noticed that, but I didn't check to see where it was pointed to.
I restarted Mail and sure enough it reset itself but now it won't save anything about its presentation. Let's say I drag a Mailbox to the shortcut bar—it will stay there until I quit the app. When I restart it it disappears and everything resets again (except the window position—if I drag the window to the left of the screen it will stay there even after being restarted). Same for opening the disclosure triangles next to the top-level items like Inbox, Sent, Drafts… They just close and reset after I restart the app.
I noticed that Mail didn't recreate the .savedState symbolic link. I found another .savedState folder in ~/Library/Containers/com.apple.mail/Data/Saved State/ (wth is this Containers directory by the way? Does it have Inception-style copies of the system in it?) and made a symbolic link to it inside ~/Library/Saved State/. Still no luck.
I’m really hoping that I can avoid wiping the system as I haven’t done that in years and would like to keep it that way as everything is set up just so.

Weird weird things… This was solved by force-quitting the 'cfprefsd' process running under my user.

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