iptables dual stack - ipv6 not working

I have problem with my iptables setup. I want to have completely dual stacked server so I use same rules for IPv4 and IPv6. However all IPv6 connections are just being dropped while IPv4 are working without any problem.

Here are all files I use to populate firewall rules: here - First file is the script I run, second contains common (shared) rules for IPv4 and IPv6 and third and forth are files containing specific rules for IPv4 and IPv6.

I want to point out that everything works perfectly on IPv4.

Problem isn't just with the services like FTP but I can't even ping the server (tested from many computers on many different networks).

Just for you to be sure, this is output of command iptables -L -n -v:

Chain INPUT (policy DROP 511 packets, 79527 bytes)
 pkts bytes target     prot opt in     out     source               destination
 1765  739K ACCEPT     all  --  !eth0  *       0.0.0.0/0            0.0.0.0/0
43146 1980K ACCEPT     tcp  --  *      *       0.0.0.0/0            0.0.0.0/0            tcpflags: 0x10/0x10
  180 26305 ACCEPT     all  --  *      *       0.0.0.0/0            0.0.0.0/0            state RELATED,ESTABLISHED
  138  8300 ACCEPT     tcp  --  *      *       0.0.0.0/0            0.0.0.0/0            tcp multiport dports 20,21,25,80,443,465
    0     0 ACCEPT     tcp  --  *      *       0.0.0.0/0            0.0.0.0/0            tcp dpts:50000:50500
    0     0 ACCEPT     udp  --  *      *       0.0.0.0/0            0.0.0.0/0            udp dpt:1194
    0     0 ACCEPT     icmp --  *      *       0.0.0.0/0            0.0.0.0/0            icmptype 0
    0     0 ACCEPT     icmp --  *      *       0.0.0.0/0            0.0.0.0/0            icmptype 3
    0     0 ACCEPT     icmp --  *      *       0.0.0.0/0            0.0.0.0/0            icmptype 4
    0     0 ACCEPT     icmp --  *      *       0.0.0.0/0            0.0.0.0/0            icmptype 8
    0     0 ACCEPT     icmp --  *      *       0.0.0.0/0            0.0.0.0/0            icmptype 11
    0     0 ACCEPT     icmp --  *      *       0.0.0.0/0            0.0.0.0/0            icmptype 12

Chain FORWARD (policy ACCEPT 0 packets, 0 bytes)
 pkts bytes target     prot opt in     out     source               destination

Chain OUTPUT (policy ACCEPT 11171 packets, 65M bytes)
 pkts bytes target     prot opt in     out     source               destination

and this is the output of command ip6tables -L -n -v:

Chain INPUT (policy DROP 32 packets, 3076 bytes)
 pkts bytes target     prot opt in     out     source               destination
    8   832 ACCEPT     all      !eth0  *       ::/0                 ::/0
    0     0 ACCEPT     tcp      *      *       ::/0                 ::/0                 tcpflags: 0x10/0x10
    0     0 ACCEPT     all      *      *       ::/0                 ::/0                 state RELATED,ESTABLISHED
    0     0 ACCEPT     tcp      *      *       ::/0                 ::/0                 tcp multiport dports 20,21,25,80,443,465
    0     0 ACCEPT     tcp      *      *       ::/0                 ::/0                 tcp dpts:50000:50500
    0     0 ACCEPT     udp      *      *       ::/0                 ::/0                 udp dpt:1194
    0     0 ACCEPT     icmpv6    *      *       ::/0                 ::/0                 ipv6-icmptype 129
    0     0 ACCEPT     icmpv6    *      *       ::/0                 ::/0                 ipv6-icmptype 1
    0     0 ACCEPT     icmpv6    *      *       ::/0                 ::/0                 ipv6-icmptype 128
    0     0 ACCEPT     icmpv6    *      *       ::/0                 ::/0                 ipv6-icmptype 3
    0     0 ACCEPT     icmpv6    *      *       ::/0                 ::/0                 ipv6-icmptype 4

Chain FORWARD (policy ACCEPT 0 packets, 0 bytes)
 pkts bytes target     prot opt in     out     source               destination

Chain OUTPUT (policy ACCEPT 0 packets, 0 bytes)
 pkts bytes target     prot opt in     out     source               destination

Ouput of iptables-save:

*filter
:INPUT DROP [93:13846]
:FORWARD ACCEPT [0:0]
:OUTPUT ACCEPT [4788:4752203]
-A INPUT ! -i eth0 -j ACCEPT
-A INPUT -p tcp -m tcp --tcp-flags ACK ACK -j ACCEPT
-A INPUT -m state --state RELATED,ESTABLISHED -j ACCEPT
-A INPUT -p tcp -m tcp -m multiport --dports 20,21,25,80,443,465 -j ACCEPT
-A INPUT -p tcp -m tcp --dport 50000:50500 -j ACCEPT
-A INPUT -p udp -m udp --dport 1194 -j ACCEPT
-A INPUT -p icmp -m icmp --icmp-type 0 -j ACCEPT
-A INPUT -p icmp -m icmp --icmp-type 3 -j ACCEPT
-A INPUT -p icmp -m icmp --icmp-type 4 -j ACCEPT
-A INPUT -p icmp -m icmp --icmp-type 8 -j ACCEPT
-A INPUT -p icmp -m icmp --icmp-type 11 -j ACCEPT
-A INPUT -p icmp -m icmp --icmp-type 12 -j ACCEPT
COMMIT

Output of ip6tables-save:

*filter
:INPUT DROP [6:778]
:FORWARD ACCEPT [0:0]
:OUTPUT ACCEPT [0:0]
-A INPUT ! -i eth0 -j ACCEPT
-A INPUT -p tcp -m tcp --tcp-flags ACK ACK -j ACCEPT
-A INPUT -m state --state RELATED,ESTABLISHED -j ACCEPT
-A INPUT -p tcp -m tcp -m multiport --dports 20,21,25,80,443,465 -j ACCEPT
-A INPUT -p tcp -m tcp --dport 50000:50500 -j ACCEPT
-A INPUT -p udp -m udp --dport 1194 -j ACCEPT
-A INPUT -p ipv6-icmp -m icmp6 --icmpv6-type 129 -j ACCEPT
-A INPUT -p ipv6-icmp -m icmp6 --icmpv6-type 1 -j ACCEPT
-A INPUT -p ipv6-icmp -m icmp6 --icmpv6-type 128 -j ACCEPT
-A INPUT -p ipv6-icmp -m icmp6 --icmpv6-type 3 -j ACCEPT
-A INPUT -p ipv6-icmp -m icmp6 --icmpv6-type 4 -j ACCEPT
COMMIT

If I try to ping the server over IPv6 (ping -6 2a02:2b88:2:1::2498:1) then I get Request timed out. If I try to ping it on the server (over SSH), then It ping's without any problem:

ping6 2a02:2b88:2:1::2498:1 --> 64 bytes from 2a02:2b88:2:1::2498:1: icmp_seq=1 ttl=64 time=0.034 ms

OR

ping6 localhost --> 64 bytes from localhost: icmp_seq=1 ttl=64 time=0.031 ms

I also forgot to mention that if I change whole INPUT chain to ACCEPT then everything works. Of course this is unfortunately not an option ...