While you've still got a few hours for bug smashing, autocollect stopped working for me after the second upgrade. This is such an interesting idea, it really broke my brain!
Thank you for the kind words! I think the problem stemmed from the timer starting when you bought the upgrade, but not checking if you bought the upgrade again when the main scene is instanced. Now when it starts it checks if the upgrade is bought and hopefully starts accordingly! Thanks for the report!