Hello pauls73,
Thanks for that info and choosing the Apple Support Communities. I know how important getting Notifications on your Mac working how you need is to you! The good news is the following article shows that you can sort Notifications by Recents, Recents by App and Manually by App:
OS X El Capitan: Notifications preferences
If that is set correctly and you're still having an issue, your next step use Safe Mode to start up your Mac so that it performs certain checks, delete system cache files, verifies your startup disk, and attempts to repair directory issues if needed. Test in Safe Mode, then restart your Mac normally and test the issue again.
Try safe mode if your Mac doesn't finish starting up
Limited graphics performance in OS X recovery or safe mode
Cheers!