For anyone who can't play due to the persistent data, here's how to fix it.
Open the directory where you have the game's executable. Open the 'game' directory. Open the file 'script.rpy' in the text editor of your choice. Locate line 254 and 255. It should look like below:
if persistent.its_over == True: return
Edit it so it looks like this:
if persistent.its_over == True: $ persistent._clear(False) return
This will make it so you clear all of the saved data when you run the game. You will have to click Start twice, once to run the new code and a second to start the game.
Unfortunately, I think this goes against what the author was intending, but it will let you play until an official fix is made.
Edit - It's probably obvious, but I'll say it anyway - you need to save the 'script.rpy' file before running the game.