When comment tokens are being processed, the instance always fails because the bundle is being set to 'comment_body'. My debugger shows that we ought to be setting this to $comment->node_type, though Im not sure if thats just my scenario or not.
I believe the call to text_sanitize will always get a null instance, and therefore simply call check_plain instead of running it through the designated filters.
Here's the offending line.
http://drupalcode.org/project/drupal.git/blob/dce3c77a61d9510dbac6927b60...