I found a workaround, and possibly the cause of the crash! 
Opening the maker pen (while advanced creation mode is enabled) in the special MakerAI dorm room works for some weird reason (that said, the first time I try to take it out, it gets dropped on the ground instantly. 2nd time it works).
After succesfully opening my maker pen, I went back to a normal dorm without changing anything. It starts glitching again (same in R1.0 room or R2.0 room).
I went back to MakerAI dorm, it works again.
Then I turned off random settings 1 by 1 and went back and forth between the MakerAI dorm and my dorm, to find out that turning off “Allow full screen config menu in Advanced Creator Mode” resolve the issues I had in other rooms!
After turning off that option, I also don’t have the other weird glitch where my maker pen drops on the floor the first time I try to take it out in the MakerAI dorm.
I also tried turning this setting back on and after switching room, my maker pen is broken again.
So I’m 99% sure this setting is somehow the source of the cause of my maker pen crashing.
(Also very minor thing, sometimes this mode is called Advanved CreatION mode, some other times Advanced CreatOR mode.
