I doubt the reason why your variables are being cleared is because of skript. Keep in mind there are thousands of other players who are using the same version of skript, and majority of them don't experience this problem, for example, me. I have heard a few things about variables being reset on server restart, some people think it's because the world name has an underscore in it, and other people think it might just be an error with skript and to reinstall it.