Hmm, so I did a replay again and got the to end of this version...and I noticed there isn't any way to exit this title, so I was forced to do a ctrl-alt-del to close the Ren'py program (I could also change the setting to window mode, then close that way).
I have also attached images below showing what I see after I completed the update… The first images shows it's missing the go back to the main menu, or close program choices, it only has a preferences choice.
Also I'm not sure if the Joker walk through mod could be affecting the lack of menu choices, but as you can see after I chose the bottom right preferences button (second image), it shows a lot of blank spaces where other choices are usually shown.