Ok, I'll quote this from the Skype 8 electron user's guide in the scripts features section:
"The JAWS virtual cursor is turned off each time Skype 8 takes focus, to simplify navigation. The built-in JAWS Skype 8 scripts also do this as of this writing. Use Ins+Z while in Skype if you want to turn the virtual cursor on or back off manually."
I sincerely never activated virtual cursor from within Skype so I don't know for sure the problems in such a case; what I assume though is that if the scripts behave like this there must be a reason.