Thanks for your help. Yeh I noticed the duplicate custom js, so I have been trying to comment it out, which is how I noticed the saving issue.
After you deactivated the plugins I commented out the js and that seemed to save ok. I then enabled both plugins again and one of their caches must have replaced the most recent cornerstone version, so the custom js was back to how it was before…
I then deactivated both WP Super Cache and Autoptimize but I still wasn’t able to save changes to the custom js. I have now removed both plugins and still have the same problem.
Am I missing something? Did you do anything else, other than deactivate those 2 plugins in order to get it to work?
Thanks!