Always interesting to read these posts about Scramble, Wiebo. I had a similar problem with GMS 2 when I wrote my first game using that. I had lots of separate objects all off doing their own thing and no dedicated game handler object to keep track of them all. It caused all sorts of wild problems with controlling instances of objects to update them with information from other objects to try and keep everything working correctly, even for something simple like a Pause mode.
I learnt a lot from doing a bit of research before I started the next game as it's so much simpler to avoid future problems when you make sure you know what you're doing first.
Good luck with what you're doing.