Pagebuilder broken after update to WP 4.1

Hi,

I recently upgraded a wordpress installation from 3.5.1 to 4.1 and it has broken the page builder. When I click on a column in the pagebuilder I get the edit window, but the content is hidden and I get the following javacsript error:

GET https://simul8.com/simul8healthcare_staging/wp-includes/js/tinymce/plugins/inlinepopups/plugin.min.js?wp-mce-4107-20141130 404 (Not Found)
wp-tinymce.php?c=1&ver=4107-20141130:5 Failed to load: https://simul8.com/simul8healthcare_staging/wp-includes/js/tinymce/plugins/inlinepopups/plugin.min.js
wp-tinymce.php?c=1&ver=4107-20141130:5 GET https://simul8.com/simul8healthcare_staging/wp-includes/js/tinymce/themes/advanced/theme.min.js?wp-mce-4107-20141130 wp-tinymce.php?c=1&ver=4107-20141130:5 ewp-tinymce.php?c=1&ver=4107-20141130:5 (anonymous function)wp-tinymce.php?c=1&ver=4107-20141130:3 awp-tinymce.php?c=1&ver=4107-20141130:5 r.loadScripts.hwp-tinymce.php?c=1&ver=4107-20141130:5 r.loadScriptswp-tinymce.php?c=1&ver=4107-20141130:5 r.loadQueuewp-tinymce.php?c=1&ver=4107-20141130:10 twp-tinymce.php?c=1&ver=4107-20141130:10 N.renderwp-tinymce.php?c=1&ver=4107-20141130:10 rwp-tinymce.php?c=1&ver=4107-20141130:10 (anonymous function)wp-tinymce.php?c=1&ver=4107-20141130:3 awp-tinymce.php?c=1&ver=4107-20141130:10 awp-tinymce.php?c=1&ver=4107-20141130:3 a.bindwp-tinymce.php?c=1&ver=4107-20141130:5 f.bindwp-tinymce.php?c=1&ver=4107-20141130:10 v.initscript.js?ver=4.1:563 (anonymous function)load-scripts.php?c=1&load[]=jquery-core,jquery-migrate,utils,plupload,json2&ver=4.1:2 m.Callbacks.jload-scripts.php?c=1&load[]=jquery-core,jquery-migrate,utils,plupload,json2&ver=4.1:2 m.Callbacks.k.addscript.js?ver=4.1:562 contentEditorscript.js?ver=4.1:552 (anonymous function)
wp-tinymce.php?c=1&ver=4107-20141130:5 Failed to load: https://simul8.com/simul8healthcare_staging/wp-includes/js/tinymce/themes/advanced/theme.min.js

I am currently trying to disable all plugins in an attempt to diagnose the issue. When I try to disable any of the following three plugins:

Revolution Slider
LayerSlider WP
Envato WordPress Toolkit

I get a message confirming they have been disabled, but they are still on the ‘active’ tab of the plugins page. Disabling them in the database just results in the value for active_plugins being overwritten, enabling all 3 plugins again.

Does anyone have any advice or tips on diagnosing this issue? Are any of the above plugins known to interfere with v4.1? All 3 plugins are fully up to date.