Hi Claesbjo,
global preferences are saved in Cubase’s preferences folder, not in the .cpr file. The actual issue here is that this particular setting should be a project setting, because it changes the sound of your mix. That is the reason why the setting goes back to default every time, because it can’t be saved in the project and, again, it is not a global setting!
Nevertheless our developers are investigating the possibility of a different solution.
Regards