I did do that based on my research. And I've manually double checked the permissions in Terminal.
I'm trying this to see if the settings stick:
Quit all apps Set the Search Scope in Alfred Shut down the computer Start the computer
I'll let you know if this procedure has cured this. I seem to recall other plist settings where I've had to do something similar to make them stick for whatever reason. While I couldn't confirm it, the loss of search scope (and only search scope) seemed to be associated with sleep/wake.