I was having the same problem and believe it or not the following is what finally resolved it for me:
Checking both the "[x] Email" AND "[x] Web" options in the GitHub Notifications center of my GitHub Account Settings:
1. Login to your GitHub account.
2. Click the Account Settings icon on the top right.
3. Click the Notifications center category in the left column.
4. Make sure BOTH the "Email" AND "Web" options are checked.
5. Make sure the correct email address set to receive notifications.
In my case, I only had "Email" checked, but not "Web" (since I prefer doing everything via email rather than via crappy web page interfaces), and was never receiving any Email notifications (even though I had the "Email" option checked!).
But as soon as I checked the "Web" option as well (so that BOTH options were checked), VOILA! I began receiving my email notifications again.