I'm having the same issues, also with an Airport Express as tunnel endpoint. Netalyzr gives:
Your system can not send or receive fragmented traffic over IPv6. The path between our system and your network has an MTU of 1381 bytes. The bottleneck is at IP address 2001:470:0:7d::2. The path between our system and your network does not appear to handle fragmented IPv6 traffic properly.
The interesting part is that these issues only started about a week ago. Before that, everything worked fine for months.