It would help if you could post specific examples of what's not working. That might help identify problems with locate, with your locate.db, or some other error.
As is stands, I can't get locate to fail on locating files in the directories you mention:
% locate com.apple.timezone.auto.plist
/Library/Preferences/com.apple.timezone.auto.plist
or:
% locate com.apple | grep ^/Library/Preferences/
/Library/Preferences/Audio/com.apple.audio.DeviceSettings.plist
/Library/Preferences/Audio/com.apple.audio.SystemSettings.plist
/Library/Preferences/Logging/Subsystems/com.apple.WebInspector.plist
/Library/Preferences/SystemConfiguration/com.apple.AutoWake.plist
/Library/Preferences/SystemConfiguration/com.apple.Boot.plist
/Library/Preferences/SystemConfiguration/com.apple.accounts.exists.plist
/Library/Preferences/SystemConfiguration/com.apple.airport.preferences.plist
... plus many more
The other caveat that comes to mind is permissions. As per man locate:
The locate database is typically built by user ``nobody'' and the locate.updatedb(8) utility skips directories
which are not readable for user ``nobody'', group ``nobody'', or world. For example, if your HOME directory is
not world-readable, none of your files are in the database.
So maybe the files you're looking for are in directories that are not readable to the daemon.