In past the Xliff adapter used the source string as message Id. According to the Xliff standard the trans-unit Id should be used. This behaviour was corrected with Zend Framework 1.10. Now the trans-unit Id is used as message Id per default.
But you can still get the incorrect and old behaviour by setting the
useId option to
$trans = new Zend_Translate( 'xliff', '/path/to/source', $locale, array('useId' => false) );