Dan, this was a feature we added before we included inline images as attachments of the overall reply and ticket. Because of this, we are going to remove the references from the text reply and will be in the next build. In addition to inline images being attachments they still exist in the HTML reply which can be viewed via the "Show HTML".
The next question people ask is why we don't show the HTML versions of replies in the ticket conversation. It is absolutely critical to show as much of a ticket conversation as possible so we strip absolutely everything we can to show the actual content while providing the ability to see replies in their original view (HTML / Images etc).
Hope this helps,
Tim Uzzanti
CEO
SmarterTools Inc.
www.smartertools.com