It's similar to JS which complex button handling. Basically the Esc key is being picked up by both the menu and the scene when the menu clears.. Hard to diagnose if you can't repeat it though.
What version are you using? I just migrated my game from 4.0.3 to 4.1.1 no problems, but definitely if you are using a 3.x version I would not recommend updating because a bunch of syntax things have changed and it may kill your existing code till you go through and fix all the little nuances.
I responded to one of your posts on reddit too, if you want to collab on this or need someone to test a solution for you I'd be happy to help out. my reddit account has the same name. I also post in r/binkgolf almost daily so you can find me there. I've briefly noticed a couple little glitches that I recognize because I've had them show up in my games too.