I've noticed that a) it's only w/ Chrome and b) it only happens when I have two seperate instances of Chrome running. As you can see from this screenshot with the desktop preview active, the window I'm on (desktop 2, where I took the screenshot) it seems that dexpot has lost the window--even though Chrome is clearly open, it doesn't show in the desktop preview.
When I switch to any other desktop and switch back, Chrome appears in the taskbar, but is in the lower-right-hand-corner. The only way for me to get control of it is go to the taskbar, hover over the Chrome taskbar items, see the window preview for the window that's hidden in the corner, right-click on it, select "Move", hit an arrow key, and then move my mouse.
I think one way of getting Dexpot to "find" the window is by doing the same as above, but instead of hitting "Move", select "Dexpot" instead, and then move (to any desktop). I need to test more, but I think that makes dexpot reacquaint itself with the lost window.