You were right about that I just messed around with it and got the same result. It was pretty much using a save file that was never going to be saved after you load a new one.
(╯°□°)╯︵ ┻━┻
(The only way around this would be to relaunch the game)
I made another update and it should hopefully be fixed now (fingers crossed)
Thanks for pointing it out once again, it would be a huuuuuge problem if it slid its way into late development like you said.