My setup is brand new raspbian install (Jan 11 2017 build) and using one-step automatic install. I picked Google upstream and blocking both IPv4 and IPv6. I'm using ethernet.
After I update the settings on my router like this
Have you tried disabling IPv6 on your router to see if it would work if everything goes via IPv4? (only a question, not recommending to disable IPv6 for all time from now)
Could you generate a debug log (pihole -d) and provide the token to help us assisting you?