sorry for giving you such a run around with this one! this shouldn't be important if it's very rare, but in case it's bothering you let me give as much more detail as I can:
I started the game for the first time that day (having played 2h48m on previous days), watched the entire opening cutscene, and then went into a second file without launching the first one. Then I played for ten minutes, doing a lap of the left area before heading to the right area where you can first save the game. Then I saved, went down the elevator, walked into a thorns on purpose, and promptly quit. Then I looked at the saves and they were strange so I told you about it. I later played more on my first save, and my second save (which I haven't touched since) has remained at 2h58m while my first save progresses as normal.
Wow , thats really detailed and helpful.
But you don't have to be sorry this is not really a run around compared to other bugs that appeared after Game Maker Updates and took weeks to solve because they had nothing to do with my code and even if it was a run around, it's my fault because this bug has most likely to do with the way I programmed the savesystem.
I can't tell if it is rare. I couldn't recreate it but that doesn't mean it won't happen to others. I really hope it is rare.