Drush cache-rebuild breaking menus
EDIT: I take it back. The problem has started again in drush 8.1.8 when Drush cr is used in a script - we have it in a back up script to reduce the size of the DB before pilling a copy of it - the application of the is-Active tag is getting broken on menu elements and any styling - say turning on or off visibility to expand the menu - seems to to totally break. 

Manually clearing the cache through the UI fixes the issue but is not ideal 

Drush 8.1.8 seems to have fixed the problem. I have looked through the change log though and cannot see what got changed in regards to the cache-rebuild that would fix the problem but it seems to have gone away so...