I spent the last few hours scratching my head over why I couldn't get IPv6 working... the main problem was a total block of traffic in the direction of LNS --> CPE.
Running Wireshark on the LNS' tun0 showed ICMPv6 requests arriving from the CPE and being replied to by the LNS although the CPE didn't show these packets as being received.
After backing up my config at both ends, I tried lots of stuff eventually ending in removing the throttling for this session (reason: it is provisioned as 24Mbit/s by the telco but throttled down to 8Mbit/s) and IPv6 connectivity worked in both directions.
Putting the config back to sane defaults (incl. throttling) and then removing the throttling demonstrated that this was definitely the case.
Throttling works perfectly with any IPv4 traffic; so there are no problems there, or with IPv6, just so long as they are not running in unison.
I can be mailed at email@example.com (ROT13'd to protect against spam!) but I'm happy to test any patches or help to debug this further.
I would also be interested in implementing a patch for this but would appreciate a quick explanation as to the 'journey of a packet through l2tpns' so I know where to concentrate my efforts.