Problem with tag <code> always disappear on Drupal CKEditor? Try to disable Advanced Content Filter (ACF)
Start from CKEditor 4.1 , it has core feature that limit HTML code, configurable Advanced Content Filter (ACF).
If you have special use of HTML tag, for example tag <code> on syntax highlight, you have to change the ACF configuration, so the tag won't be stripped everytime you save your Drupal node.
Change it on Menu Configuration > CKEditor > Full > Advanced Content Filter. (shown on image)