Did you update WP to 4.5 before this issue started?
Also did you try and just use the Widgets page under Appearance and NOT use the Customizer?
Just a few thoughts.. I love this plugin.
I am using this plugin before WP 4.5 VER release and issue too. After updated to WP 4.5, I had deleted the plugin and re-installed it. But the problem is still there. I can’t able to work on it. It’s not showing apply button. When I made some changes in the widgets, it shows loading icon instead of apply button and all the its loading and loading… Can’t able to use it.
Can’t help you … but on my site I see NO Apply button,
there is just the save button on the bottom of the widget flyout. Try using the dynamic widgets on the Appearance – Widgets page, not in the Customizer.
I also tried to do it from Widgets Page. After clicking on save button, loading icon displaying near save button which is not working except loading and loading. Save button only save after De-Activating Display Widgets Plugin By Strategy11 but after that it is only saving in the wordpress and of course it will not display option button for where I can Show Or Hide on the page since the plugin is de-activated. I don’t know how to configure it. Just frustrate with the issue.