Comment links don't work

It seems that the links to the comments don't actually link to the comment, only to the original topic. I tried using the patch for link_alter that was posted for 6.x-1.dev, but that didn't change anything. (I will admit that coding baffles me, so perhaps that has nothing to do with it.) The issue is that the link that is created by the comment title is something like: drupal6_11/node/85#comment-2 ; but the actual link to the comment is: drupal6_11/node/85/2#comment-2. It seems like the construction of the link gets messed up. Is this a conflict with other settings I have? Any help would be appreciated. I really like the module.