Stiffler,
I'm not too familiar with JComments, but the below may work for you. I'm really not sure why the 2 different URLs are being generated by Joomla, but the code below will hopefully help you to create a unique URL for each link:
{JFBCComments width=550 href=<?php echo JRoute::_('index.php?option=com_content&view=article&id='.JRequest::getInt('id')); ?>}The above is basically just trying to create the URL for the current page using some of the information from the URL, but doing so dynamically, so that you can add it to the template file like you're trying.
Hope that helps, but if you have any questions, or run into other issues, let us know!
Alex