Unfortunately, I have to re-write this because when trying to upload an attachment, it navigated away from this page and lost everything I wrote. So this version will be shorter.
I am experiencing the same symptoms. I'm also using Karabiner to map Caps Lock to F19. I successfully reassigned the hotkey, but it didn't make a difference, despite being updated in the Preferences UI. My theme preference and menu bar preference are also not being reflected.
Screenshots: http://d.pr/i/bEzx, http://d.pr/i/wzxP Update:
I had originally quitted Alfred from Alfred Preferences > Quit Alfred Preferences. (which I'm now seeing is not quitting Alfred) and quit Alfred directly and now my settings are being reflected.
