Solved: How do I allow all tags in CKeditor
UPDATE:
A fix for multisites and Aegir setups will come out in CiviCRM 4.7.21.
See https://issues.civicrm.org/jira/browse/CRM-19303

After much work we managed to solve this. It was definitely a multisite / Aegir issue.

We had to go through some hoops and down some rabbit holes but you can find our solution detailed here: Solved: Is this a bug - [civicrm.files] variable