I did a little testing of my own here... what I found is that I experience the whole Tk window disappears until I hit Enter if I start the application from the CLI window directly.

If I double-click on the script within the UI, the Tk window re-appears properly without having to hit enter.

I've got to run so I can't test further right now, but I do know that win10 had some new registry settings added related to the cmd.exe program, so that might be worth having a look at. I'm absolutely unsure about this, but if it is a registry setting, you may even be able to have your script modify it on the fly using Win32::Registry (my experiences with Windows is that changing anything requires reloading whatever you're trying to modify though).