Thanks for the clarification

Same reason as here: [FAQ] Some windows appearing on all desktops on Vista/7/8.

After playing a little bit more with the problem, it seems that starting Setpoint as administrator fixes the problem (I have no idea why, though)

Sorry for the really late answer - yes, I have the "Run as administrator"-option checked. (Manually starting as administrator doesn't change anything, too)

Do you run Dexpot as administrator?

I have this issue as well. I have desktop switching mount to my F7 and F8 keys and have two buttons on my mouse bound to F7 and F8 so that I can flip desktops with my mouse. When I switch to an empty desktop (no active windows) or to a desktop without any windows in focus I can't switch to another desktop until I either the desktop or an out-of-focus window. The odd thing is that when I press F7 or F8 on the keyboard the problem doesn't occur, which makes me think it's actually a problem with the mouse software. I use Logitech setpoint which I have had issues with in the past. I wouldn't be surprised if it was the source of this problem.

When I first installed Dexpot, I used the "horizontal-scroll-to-switch-desktop-feature" from the mouseevents plugin to switch between desktops, and it worked pretty well. But after I installed the SetPoint-software for my Logitech mouse, this function stopped working reliably. After a few hours of searching I managed to bind CTRL+LEFT to the mousewheel, which seems to work.
There's just one little problem (I think it was there even before SetPoint, but now it's more noticable): The keystrokes are only registered properly by Dexpot if a window is focused - that means that after switching to an empty desktop, I have to open a window or focus the desktop by clicking on it to make it work again.
Would it be possible to simply focus the desktop if no window exists that can be focused? This should remove all issues related to any customised buttons on my mouse (not only those used for Dexpot)