We have translations in Transifex that will never be pulled in to their respective modules until the those modules are configured properly.
Steps to do this:
1) Make sure that the .tx/config file in the module references all languages we currently support (see example below)
2) Make sure config.xml references all languages we currently support (see example below)
3) Run "tx pull" to create all the messages_*.properties files for all languages
4) Commit these changes
An example .tx/config and config.xml that are properly set up (at least with all languages we support to-date can be found here):
***WARNING: be sure when cut-and-pasting the example .tx/config file not to include the slug line (ie [OpenMRS.appointmentschedulingui-module]). If a config file references the wrong module, when Transifex does it's automated nightly update, it will overwrite all translations for that module, and any that haven't been committed to github will potentially be lost forever***