H'm, where are you trying to make a save (or where were you trying to make it when it broke)? This sounds like an issue where the save is occuring on a screen where it shouldn't, which would make the default last passage (the variable that's meant to return you to the story) the main menu. That's a big oopsie in the game code somewhere.
Im on an Android , Chrome, and the passage is where Siruud asks you to unbind him BUT I just tried saving a couple times during the common route today and it worked completely fine. The saves that weren't loading properly before are also now loading properly, so I have no clue what happened there. I think it might've just been an issue on my end? Thank you anyway for trying to help!!