OK I figured out what the problem was, the solution can be found here:

viewtopic.php?f=21&t=1848

Just to clarify, basically there is one program that stays open on all desktops no matter how many desktops I set up. So it doesn't seem to be a monitor issue, it is a program issue.

Hello, I'm using dual monitors (Laptop connected to an extra monitor). I have set the monitor to be an extension of the main laptop screen. When I try to switching desktops with Dexpot only the main laptop screen switches but the extended monitor remains the same. When I look at how the windows are ...