I followed the knowledge base to get it working: http://www.magentocommerce.com/knowledge-base/entry/ee1141-ce191-responsive-email#hi-rez-logo 
Note the part "Localizing Transactional Emails",after following the previous instructions, copying to /en_UK finally got the emails on their way (including ones previously not sent), We also had a problem with the order confirmation page not being displayed to customers on completion. This was fixed also.