I'm using version 0.03 of the Virtual Desktop plugin and I seem to have occasional problems with application windows (or dialogs, or menus) leaving "shadows" behind, after I close them.
I'm afraid I cannot reproduce the exact behaviour that causes the problem yet, I just know that after several hours of use each virtual desktop appears to have several lines over it, which sit on top of all other applications and cannot be removed with a right-click desktop->refresh.
If I look at the "arrange virtual desktop" usually I will see something like: "NoneTitle Window [WindowClass: Main]" or something like that. In some cases I can move them to another desktop and the lines move, so I know these relate to the "shadows". I have no way of killing these processes. I do use a program called ToolBox from Cylog (http://www.cylog.org/utilities/toolbox.jsp) that has similar entries in the virtual desktop arrange window and wonder if it is the cause of the problems.
I'm using Windows XP and have turned off "show shadows" under menus and other advanced desktop effects like fading.
I'm not sure if this is related but sometimes application windows become duplicated across more than one desktop. Usually it seems to happen if an application is busy doing something i.e. using processor time and then I switch desktops before that application process has finished. To fix the problem I usually send the application back to the original desktop it was on (even though it is already there) and then I only have one instance again.
I hope all of this makes sense. Sorry that I cannot be more specific at this time but if I make any further discoveries I'll be sure to post them here.
BTW the tooltip that appears over the system tray virtual desktop icon says v0.02, but I've downloaded the latest version of DM2 1.23.1, and it says Virtual Desktop is v0.03 on the plugins setup.