To reproduce :

• Open an Atto editor
• Open the source code editor
• Paste this :

  <article>

  <header>Header</header>

  <footer>Footer</footer>

  </article>

• Disable and enable the html source code editor
• Here what we see :

  <article>

  Header

  <footer>Footer</footer>

  </article>

  This should be a valid element and so not be cleaned :
  http://www.w3schools.com/tags/tag_header.asp