Again, why do this on the command line with STDIN and STDOUT? It seems to me like more trouble than it's worth to try do what you're doing through a console interface -- which provides usually just the bare bones of character support -- particularly if you plan on doing it through something clunky like this WPS-ISE. I'm not a GUI guy at all, but it seems like it might be worthwhile to set up a simple GUI to receive the input and print the output. Have you looked at Tk? It would give you something like Windows text boxes which ought to support your Unicode fonts. You could also have a file selector dialog.

Update: Upon fiddling with it, I now see that the Tk interface that comes with ActivePerl now, at least, is Tkx. And it has crummy documentation. But I think it might help you.