If you are using 'perlapp' to create .exe files from your .pl source, you can try including '--gui' in your builds.

I posted a question related to yours earlier this month at ActiveState wondering why passing parameters when invoking 'abc.exe' programs was failing. I had been creating via 'perlapp --gui abc.pl' and my memory says that when I stopped including '--gui' in my builds, I could then pass parameters. But then I got the silly console window back.

Jan Dubois had posted back that:
Basically --gui for PerlApp has the same effect as switching from perl to wperl. If something doesn't work with wperl, then it most likely won't work with "perlapp --gui" either (and can't be fixed inside PerlApp).