Shouldn't be... I've had Vista before and the Skirmisher was running fine back then. Where do you have the game installed? "C:Program Files" or somewhere else?
That's pretty odd, actually. Never had someone complain about such a problem. So just to make sure, everything else is fine on your end:
1) You create the mission using the Skirmisher like above and hit "Create mission"
2) You start Nexus and start the mod you selected in the Skirmisher (in this case: "NEXUS Skirmisher")
3) You arrive at the mission-select screen of the game and you don't see your previously created mission in the list (like mission "test" in the following screenshot)
Correct?
Please have a look at your Nexus folder and see, if there's the
modsNEXUS Skirmisherconfig.ini. What does it say about "Mod Name" and "Mod Directory"? Furthermore, are there NO files in
modsNEXUS Skirmisheruniversemod_missions?