It sounds like a bug in our Alt+Tab Handler, so we'll try to fix it before we give up and add an Advanced Setting to just remove the Desktop from it :)
I need to do a bit of research to find out what info I'll need from you to help troubleshoot. I'll keep you posted as soon as I have more news!
Ok, we need to add some more logging info into the code so that we can see what's happening when they get shuffled around. I'll let you know as soon as Beta 6 is available.
We've just released DisplayFusion 5.1 Beta 8 (http://www.displayfusion.com/Download/Beta/), and this issue should hopefully be all fixed up. We've also added an Advanced Setting to remove the Desktop from the Alt-Tab handler altogether