Notification Center stores it's settings in /var/mobile/Library/BulletinBoard
.
You probably will be interested in files SectionInfo.plist
and SectionOrder.plist
At first, try checking their permissions, it can be a possible cause of them not being saved. It should be -rw-r--r-- mobile:mobile
.
You can make backup of this files and restore them when your NC gets messed up again, or write a script and run it from terminal, something like
cp /var/mobile/Library/BulletinBoard/SectionInfo.plist_backup /var/mobile/Library/BulletinBoard/SectionInfo.plist