first of all, I really like Pi-hole and it works fine but somehow youtube is making problems. I think it's the IPv6 part that's problematic because when I remove the IPv6 address in my dns settings the video loads normally but then I get the ads that run on IPv6. With the IPv6 address set up, there's a long delay of 5-10 seconds until the video starts.
Many ad companies deliver ads through ipv6 so keep it enabled to block ads over ipv6.
I suggest you to use OpenDNS as the upstream DNS server, because most people say that you will see less ads(?).
Also YouTube has been known to cache ads. So clean your browser cache after configuring upstream DNS.
You can use uBlock extension to block these ads. Hope that it helps.
The thing is that I've already blacklisted those links. I tried a video on Opera and Internet Explorer but I still have that problem. It seems to have problems with ipv6 so maybe I have some faulty configuration on this part but I don't know enough about pi-hole to check that.
Using µBlock seems to work but I prefer to use only one of them. I mean, what did I set up pi-hole for if I could just use µBlock