Hello - This bug has existed for awhile on my system but i reboot so infrequently that it hasn't been terribly bothersome. The issue(s) occur when i reboot my Mac, on login all the prefs i've set for Alfred disappear (Alfred Hotkey, Appearance->Hide Menu Bar Icon).
I cannot remember which version of Alfred this started occurring on but I do know the issue existed in the build previous to the current 2.6 version.
OSX version: 10.9.5
Alfred version: v2.6 (374)