For some overview in my Media Library, I use the Real Media Library plugin by devowl.ip GmbH. This plugin shows a virtual folder tree. Nice for media library management.
I updated to W3 Total Cache 2.9.3 today. After that, I noticed that the Real Media Library virtual folder structure of my websites was deleted. Clearing caches did not help. I restored a backup of the site before the W3 Total Cache 2.9.3 update and voila, the virtual folder structure was there again.

I do not know the relation between W3 Total Cache and Real Media Library components. Hope that you can get a clue. I will report the issue to devowl.ip GmbH too.

Best regards,
Mark