OK, it looks like your problems are not really to do with your code or Perl at all then. I'm not really that sure what to suggest, as I've no idea how your machine is configured. And please don't take this the wrong way, but nor, to be honest, do I have time to attempt to figure it out. If you're interested in seeing what I'm getting, then send me a private msg with your email address and I'll send you over a couple of screengrabs showing (a) saving a file with greek characters from Word, and (b) what that then looks like from cmd.exe.
All I can really suggest from here is to try to nail down whatever it is that's wrong / different / unusual with your setup, possibly getting hold of someone locally who's done this kind of thing before - is there a local Perl Mongers group anywhere nearby?
Sorry I can't be of more help - good luck with sorting it out.