I'm on PC. From what I've noticed it happens as soon as the main menu loads. I can be sitting on the main menu, on the world map, talking, fighting, happens everywhere. Both idling and actively doing something.
Though, I did delete everything manually before and redownloaded it. It worked fine for a little bit (don't remember how long) but it started doing the freezes again shortly after.
I tried another game that uses Ren'Py instead and I get oddly similar symptoms.