Unfortunately, this 'select only one calendar' option only works for the actual calendar app. If you still have the 'unused' calendars on your phone, they will still show up in the notification center.
I found a way to fix this by going through all my accounts and deleting duplicate calendars. It gets a little confusing, because I have my google calendar, fb birthday calendar, outlook account, plus all the 'on my phone' and 'icloud' calendars...I managed to get them down to only 1 entry per event, but when I plugged my phone into the computer to sync, it reset to whatever settings it had been and I'm back to repeats in the notification center. I'm sure it can be permanently fixed by adjusting settings and deleting unused/repeat calendars...just haven't taken the time to do it.