I had a problem using the CKEditor with Drupal 6 where the CKEditor would not display
<code> tags properly in the editor, and would then delete trailing spaces after the
<code> tag. After some digging around, I finally found that I needed to comment out the following line in the ckeditor.config.js of my CKEditor module installation:
//config.protectedSource.push(/<code>[\s\S]*?<\/code>/gi); // Code tags
There may be other ways to work around this problem, but because I'm the only one who writes on the website, removing that line from the CKEditor configuration file isn't a big deal. If nothing else, if you're having the same problem, I hope it gives you a starting point to work from.