I decided to test the new update and the error still remains, I hope you find the bug, however if it is something very complicated I will create a new save XD
Phew, I finally realized that the true version of the game is always the latest one. Sadly, it "shows" the version of the savefile.
If you saved in v0.9.0 and loaded it to v1.0.0, the game will still be v1.0.0, no matter what it tells you.
So, false alarm. Thank you for your feedback, I'm working on the solution!