That's the intended behaviour of those two scripts:
"Swap All Windows Between Two Monitors" will ask you which monitors you want to swap the windows between (in case you have more than 2 monitors). So if you want to swap all windows between monitor 1 and 2, select monitor 1, then select monitor 2, and DF will swap all of the windows on those two monitors.
"Swap Topmost Windows on Monitors 1 and 2" will only swap the two windows on the top of monitor 1 and 2.
Unfortunately DF can't manipulate windows on virtual desktops directly at the moment. We're hoping to add support for them at some point though
Thank you Keith, In fact all is working now! Really good!
I guess there will be a lot of development for you, to include the virtual desktops deeply with DF. I was thinking about the possibilities to load directly many environments at the starter of Windows, etc... Good luck