I found the solution for this specific problem i ran into with the <i>
tag
The original answer i got from drupal forum
The fix or tweak (you name it) for it is to set the following into the ckeditors config.js:
// ALLOW <i></i>
config.protectedSource.push(/<i[^>]*><\/i>/g);
Thanks to Spasticdonkey for pointing me to the link.