When a well-formed CSV file is uploaded with relations, the terms are added to the vocabulary but the relations are not set. Instead, there are x warnings (where x is the number of terms in the csv file) like so:
Parameter 1 to taxonomy_save_term() expected to be a reference, value given in {drupal-path}\includes\module.inc on line 462.

PHP Version: 5.3.2

PS I tried this in 6.x-2.x-dev and the relations were imported properly.