Okay .. I've isolated the bug. And I'm sorry to say it's exactly what i feared. Let me give you an example of what I'm dealing with just so you can know how it happend.
Okay so when it comes to autorunning events. The priority is hardcoded and the oldest event always has priority not the one with the lowest event ID .. No not something that could actually be manipulated .. It's a simple case of seniority and it's in the reverse order of what would actually be tolerable. If older events were lower priority that would be much easier to manage XD
So in order to circumvent that I need to copy/paste the base menu events so they become 'younger' than the new cutscene events. The only trouble with that? Self .. switches. The game records self switch status in saves but THAT hooks into the event ID.
So sometimes you can end up with a self switch that was correct before getting assigned to the wrong event in a new version and completely screwing everything up XD
It's literally the most ass backwards way rpgmaker could have done this XD
Your save is a victim of that unfortunately. However I have now created a workaround which should fix this issue. I'll be releasing a patch later today which should allow you to progress as well as fix a number of other issues.
Thanks for your patience and understanding.