Hi, greetings from Germany [Europe

]
I had the same problem, and maybe there is a workaround. I dont know if it is already fixed, some with more mood can check it.
What i did/do, is to
1. change the preferences
2. save the project you are in
3. shut down the MPC
After this, my preferences are be saved. I do it about 3 times, maybe it works randomly and have nothing to do with this workflow. Its just in my mind what i did and at this time it works for me.
Excuse me for my sheep language, its not my mother speaking.
Like i said, im from germany and owner of the MPC Live I and the MPC X SE "Ultimate Bundle".....purchased my Live about 8 month ago, the X about a month.......and i love them.
MMMP