After some debugging, I found that it was due to the CSS rule.
In the skin named kama you need to change the following CSS rule in mainui.css :
.cke_skin_kama .cke_browser_ie.cke_browser_quirks .cke_contents iframe { position: absolute; top: 0; }
To:
.cke_skin_kama .cke_browser_ie.cke_browser_quirks .cke_contents iframe { top: 0; }
Depending on your setting, you may need to change it in skins/kama/editor.css
However, I recommend upgrading to a newer version of ckeditor. I found this problem on version 3.6.2.
source share