I did repair disk permissions in Disk Utility.app. After this, I did a deep reindex using this method: http://skillzdesign....using-terminal/
Still no luck. The Search finds it, but not Alfred. Even stranger, Alfred works fine for one user my Mac, but not for other one.
It just won't look in Applications or anywhere else. I can send screen shots showing "notes" in Alfred giving http://notes.app while Search finds Notes (the app).
I also in Alfred Preferences advanced, tried: Clear application cache, Rebuild OS X Metadata, and clear Knowledge.