There is a need to disable settings for CTransifex in the sh404SEF configuration (if it is installed on the site).
In the sh404SEF configuration -> 'by component' ensure that the first and fourth fields are set to 'use Joomla! router' and NOT any sh404sef routing. Failure to do so results in the links to the individual languages using strange id values and often resulting in the language translation files not being found.