I found a good answer today so I started a bounty for it. After deduction of the rep of the bounty, my net rep for today was 45. Since then it has gone to net 75 but I am not receiving any notifications.
If I click the notification button or my reputation tab, I can see the changes just fine. I am just not receiving any notifications like "+10" or "+5".
This is what my rep notification dialogue looks like:
This is what my reputation tab looks like:
So the entries are there, it's just the green "+10" notifications that are missing.