The 'messages.properties' file is not always updated by developers. There are extra codes in there which are no longer used.
Use this script: 'http://wiki.openmrs.org/display/RES/Message.properties+Utilities' to find those and clean them out.
If you read the note in the wiki page, not all messages can be pulled out immediately. Some detective work will need to be done on each code to make sure its not being used dynamically.