A pane window is a special type of window which usually acts as a toolbar or information bar, sitting on top of or next to a ‘parent’ window. When you move the parent, the pane window moves with it.
This can be a problem for virtual desktop managers because pane windows tend not to go where they are told to - they go where their parent window wants them to be.
It is for this reason that MoreDesk ignores all pane windows by default. It only bothers to represent the parent windows in the desk space view and only tells the parent window to move, letting it move any pane windows which are attached to it.
You can change this setting in the MoreDesk configuration so that pane windows are shown in the desk space view. However, you cannot click on pane windows in this view (the click will go to whatever non-pane window is behind it) and you cannot select them.
This option only exists because it gives a slightly more complete view of the desk space than without pane windows.