Drupal-7.54 , CiviCRM-4.7.16 Multi-site / Aegir platform.
On a clean Drupal+CiviCRM instal the autogenerated path for the [civicrm.files] variable in 'Settings - upload directories' differs from the URL path generated in 'Settings - Resource URL'.
In Settings- Upload Directories the civicrm.files variable is: var/aegir/platforms/platform_name/sites/siteURL/files/civicrm
In Settings- Resource URL the civicrm.files variable is: h t t p://siteURL/sites/default/files/civicrm/
The problem does not arise in a non-multi-site environment, where both paths point to 'sites/default/files/civicrm (as confirmed on the sandbox demo).
This also seems to affect the path to the files/civicrm/persist directory.
One effect of this seems to be on CKEditor: when the CKEditor configurator is used it creates files (e.g. crm-ckeditor-civimail.js) in the persist directory. But these files are ignored when CKEditor is used in Civimail (see Solved: How do I allow all tags in CKeditor, and 4.7.15 breaks civimail styles and templates (fullPage doesn't help) and maybe CiviMail template format in HTML not saving