Directory Opus is the be-all and end-all of file managers and Windows Explorer replacements, at least for me. Unfortunately, instead of running multiple instances for multiple listers, it starts a single instance and uses that to open and maintain all listers, including searches, FTP, comparisons and synchronizations.
That means it works fine in virtual windows, but trying to start it in a non-virtual window either accomplishes nothing or opens a new lister in the default desktop. One feature of Dopus is that it adds a menu item to open a new lister to the desktop right-click menu. Strangely, that menu item is also present when one right clicks on a non-virtual desktop, but the menu item doesn't do much.
Since I read somewhere that the non-virtual windows are creatures of a Microsoft API, there probably isn't a thing you can do to get Dopus to work with non-virtual windows, but I thought I would ask.
Well, I downloaded the program, but there is unfortunately nothing I can do. As you said, non virtual desktops are Microsoft creatures and third-party developers must support them to work properly. When this is not achieved, you must use non virtual desktops (that are my creatures ).
Meanwhile, I have become so addicted to the extra flexibility of virtual windows that I only keep one non-virtual desktop around in case I think of something I really want to use it for. It may not survive September.