I have very annoying problem with Windows 8. The problem is in metro control panel "PC Settings".
I don't know what is the reason for removing all apps control in the Notifications menu.
I had this problem so many times and the only fix for this that I know - is to create a new microsoft account or to do clean install (which I don't like to try those suggestions anymore).
Not sure why you have to create a new microsoft account or to do clean install. Apps can notify a user when new content arrives. Not quite sure what your problem is. Do you want to shut notifications off for all your apps? Perhaps particular apps?
Push "Show notifications from these apps" to pick on/off individually.