Try creating a blank page and adding HTML editor to it, Does the blank page have the problem?
If you cant reproduce the problem on the blank page, there will be some javascript or CSS in your site design that is causing the conflict. troubleshoot the cause by slowly removing scripts and css from the page and trying again till you find the script or css causing the conflict.
Visit the CKEditor demo page here:
http://ckeditor.com/demo
can you reproduce the problem on that page?