Wow, well after about an hour of debugging we found that vocabularies that support free tagging doesn’t work. The issue queue + patch for Drupal 6 is here http://drupal.org/node/748012 – (the issue queue is for D7, however the patch at the end is D6) In our use case we went the simple route, we changed the taxonomy to be a single option…
In any case – we tested multi-select and that does work in drupal context-6.3.x-dev… Context Variable might be a workaround as well…