This is also a symptom that hits me a lot, although with a specific application. I'm currently on "1805-wk2+ppp", with Win7.
I have the flag enabled to put all the icons on the task bar, no matter what desktop they are on. With that, I can see the preview for the missing window. I thought I'd be able to right-click on that to get the window menu, so I can "move" it, but right-clicking on the preview just makes the preview go away.
My only workaround is killing the app in Process Explorer and restarting.
If it matters, the application is an internal application that we use for instant messaging. It typically has two windows, one that lists my IM contacts, and the other a tabbed window with my conversations. At this moment Dexpot has lost track of the contacts window, although I can see the preview of it in the task bar.