The most common issue leading to the symptoms you describe is a misconfigured firewall somewhere on the path causing PMTU discovery to fail.
You can try tweaking the MTU setting on the tunnel itself. I believe the correct MTU setting for running 6in4 over PPPoE is 1476. Remember that you need to adjust the MTU setting on both ends of the tunnel. You can also experiment with lower values for the MTU setting on the tunnel. But don't go lower than 1280, which is the lowest value permitted by the IPv6 standard.
If changing the MTU on the tunnel doesn't help, you can try using ip6tables to lower the MSS on all TCP SYN packets forwarded through the router. I believe this command should work for that:
ip6tables -A FORWARD -p tcp --tcp-flags SYN SYN -j TCPMSS --set-mss 1220 I believe 1220 is the most reliable value to be using for the MSS.