I opened a bundle file in X3D. It asked for a directory to load all the files for per folder processing. After completion of the load, I closed the project without saving. The per project main name and audio folders remained after closing the project without saving. They were empty folders though. Shouldn't the folders be cleaned up as well as the audio too?

Agreed:
https://www.cakewalk.com/support/contact/problemreport.aspx
 
Let me know your issue number so I can add it to the list.
 
Cheers...

CWBRN-22619

Added... thanks...
 
http://forum.cakewalk.com/Outstanding-Issues-as-of-X3D-and-general-comments-m2952585.aspx#2952585
 

I got feedback that it is a feature request. this happens in 8.5 too.

In my opinion it's just a very trivial bug. Cleanup should be expected.
But whatever :). That's how developers think...