Yeah I got the newest version today to retest it and it still happens. I'm on Windows 10. It happens at home and at my work PC. Easy way to test is to clear data, start a new game, and start moving as soon as the screen separation starts and it'll hang after a few seconds. Sometimes it locks up indefinitely and I have to close it. I figured out how to avoid the hang by doing a very short movement as soon as the fade and then wait for the black bars to completely go off screen and then start moving.
Similarly, if I hold down a movement direction after picking up the sword while Link is holding it up, it hangs there as well. If I wait until he stops holding the sword to press any key then it's fine. I've tried all kinds of combinations of graphics settings and screen resolutions and nothing seems to help.
Thanks so much for posting these details, Shenjoku! We'd been trying to figure why the game would occasionally lag on Windows and based on your comments we fixed the issue. Specifically, your note about pressing "down a movement direction after picking up the sword while Link is holding it up" helped pinpoint the problem!
Version 2.2 is available now and should run smoothly on Windows.