The icons that are visible on all desktops are the ones stored in C:\Users\Public\Desktop. If you want to distribute them across virtual desktops, first move them to your (or all users') private desktop folder(s).

I'm trying to set up Dexpot 1.6 on a Win 7 Ultimate 64 bit computer and find that many Win desktop icons are not being seen by Dexpot so I'm unable to arrange them. Secondly, even though the Manager shows a proper selection of icons (the ones I've chosen to be on that particular screen), the actual screen has many additional icons.