Found a slight hiccup with the new late-game stage features. Will try to explain without spoilers:
When given a daily task, if you haven't taken any other actions in the facility yet, visiting the girl to perform the task results in a loop where I can only click the "let's get started" dialogue button over and over. Having trouble reproducing this one consistently so may have been some save migration one-off - I am on a v3 save which is otherwise working well.
Another minor issue: When using the downloaded version of the game via itch, going "Back to Main Menu" causes the game to crash.
I wasn't able to replicate the task issue, unfortunately, but I think I might know how it happened, and I've made a small change that I'm hoping will fix it for you. Let me know if you see it occur again!
I've also changed the buttons that load the main menu; these should work fine on the downloaded version now.