Hi time to pick this thread up 
I'm still having the same issue and soon we'll go into production use. Here is some info about my system, including the answer of the question:
lsmod | grep ^ip6
ip6t_REJECT 38788 0
ip6table_mangle 37632 45
ip6table_filter 37760 45
ip6_tables 50880 2 ip6table_mangle,ip6table_filter
uname -r
2.6.18-92.1.13.el5.028stab059.6
cat /etc/vz/vz.conf | grep ip6
## IPv6 ip6tables kernel modules
IP6TABLES="ip6_tables ip6table_filter ip6table_mangle ip6t_REJECT"
Still I get this error inside the container:
ip6tables v1.4.0: can't initialize ip6tables table `filter': Invalid argument
Perhaps ip6tables or your kernel needs to be upgraded.
FATAL: Could not load /lib/modules/2.6.18-92.1.13.el5.028stab059.6/modules.dep: No such file or directory
Ping etc works just like it should:
ping6 ipv6.google.com
PING ipv6.google.com(2001:4860:0:1001::68) 56 data bytes
64 bytes from 2001:4860:0:1001::68: icmp_seq=1 ttl=55 time=259 ms
Does anyone know what it might be or if there is any more info I can provide to make it easier to find.