The catch is that the app is not a console app, so SSH is not adequate.

If you have the privileges to get to the remote command line via SSH, then issuing the command for the gui app. from that command line will launch the app.

To have the command line not return control until the gui app finishes use start /wait. Eg.

start /wait notepad
[download]

The app will launch, and the command prompt will not return until the app is closed.

This will probably work via something like Net::SSH::W32Perl, but I have no experience of that module.