When I have RTMedia Pro enabled on my site, it prevents the plugin “Custom Sidebars Pro” by WPMUDev from working. Disable RTMedia Pro, and Custom Sidebars Pro works. I have tried re-saving permalinks.
It also causes a conflict with Ninja Forms - when RTMedia Pro is enabled, the java-based feature that allows you to export form submissions from Ninja Forms does not work. Disable RTMedia pro, and the exports work.
It might be of interest that RTMedia (with no add-ons) works normally and does not cause the conflict.
I can allow you to login to my site if you wish.