Footnote appears within text body

I read this thread for the Drupal 6.x version of footnotes where the footnotes are appearing within the body text instead of after it. Please see my attached file that shows I'm having the same issue.

I am using the Filtered HTML format which has this Filter processing order:

• Footnotes
• Freelinking
• Convert URLs into links
• Limit allowed HTML tags
• Convert line breaks into HTML (i.e.
  and

  )

• Correct faulty and chopped off HTML