Well I had some time to investigate further after posting here, and it turned out that this indeed has to to with MTU sizes.
I am using Windows XP/2003 machines on the LAN, so I don't know if this also happens with *nix OSes.
The SixXS tunnel has an MTU of 1280 by default, while Windows is using the default 1500.
As soon as I set the MTU for IPv6 to 1280 on the Windows machines, the IPV6-FRAG blocked entries disappear.
This mostly happened with UDP packets. I'm running a freenet 0.7 node.
Just in case you still want to know, here's the ipv6 filters from /status.php - I hope this is enough. Changed my Tunnel's address to 1234:5678:200... and the subnet to 1234:5678:5c1::/48 in this copy
unparsed IPv6 ipfilter rules
# loopback
pass in quick on lo0 all
pass out quick on lo0 all
# allow link-local traffic on LAN
pass in quick on vr0 from fe80::/10 to fe80::/10
pass out quick on vr0 from fe80::/10 to fe80::/10
# allow access to DHCPv6 server on LAN
pass in quick on vr0 proto udp from any port = 546 to ff02::1:2 port = 547
# allow link-local traffic on opt1
pass in quick on fxp1 from fe80::/10 to fe80::/10
pass out quick on fxp1 from fe80::/10 to fe80::/10
# allow access to DHCP server on opt1
pass in quick on fxp1 proto udp from any port = 546 to ff02::1:2 port = 547
# allow essential ICMPv6 messages: router and neighbor soliciation/advertisement
pass in quick proto ipv6-icmp from any to any icmp-type 133
pass in quick proto ipv6-icmp from any to any icmp-type 134
pass in quick proto ipv6-icmp from any to any icmp-type 135
pass in quick proto ipv6-icmp from any to any icmp-type 136
pass out quick proto ipv6-icmp from any to any icmp-type 133
pass out quick proto ipv6-icmp from any to any icmp-type 134
pass out quick proto ipv6-icmp from any to any icmp-type 135
pass out quick proto ipv6-icmp from any to any icmp-type 136
# also allow ICMPv6 destination unreachable, packet too big (PMTUD) and time exceeded
pass in quick proto ipv6-icmp from any to any icmp-type 1
pass out quick proto ipv6-icmp from any to any icmp-type 1
pass in quick proto ipv6-icmp from any to any icmp-type 2
pass out quick proto ipv6-icmp from any to any icmp-type 2
pass in quick proto ipv6-icmp from any to any icmp-type 3
pass out quick proto ipv6-icmp from any to any icmp-type 3
# allow ping to make tunnel broker happy
pass in quick proto ipv6-icmp from any to 1234:5678:200:831::2 icmp-type 128
pass out quick proto ipv6-icmp from 1234:5678:200:831::2 to any icmp-type 129
# WAN spoof check
block in log quick on gif0 from 1234:5678:5c1:0:0:0:0:0/64 to any
block in log quick on gif0 from 1234:5678:5c1:1:0:0:0:0/64 to any
block in log quick on vr0 from ! 1234:5678:5c1:0:0:0:0:0/64 to any
block in log quick on fxp1 from ! 1234:5678:5c1:1:0:0:0:0/64 to any
# Stop site-local on the outside interface
block in log quick on gif0 from fec0::/10 to any
block in log quick on gif0 from any to fec0::/10
# Disallow "internal" addresses to appear on the wire.
block in log quick on gif0 from ::ffff:0.0.0.0/96 to any
block in log quick on gif0 from any to ::ffff:0.0.0.0/96
# Disallow packets to malicious IPv4 compatible prefix.
block in log quick on gif0 from ::224.0.0.0/100 to any
block in log quick on gif0 from any to ::224.0.0.0/100
block in log quick on gif0 from ::127.0.0.0/104 to any
block in log quick on gif0 from any to ::127.0.0.0/104
block in log quick on gif0 from ::0.0.0.0/104 to any
block in log quick on gif0 from any to ::0.0.0.0/104
block in log quick on gif0 from ::255.0.0.0/104 to any
block in log quick on gif0 from any to ::255.0.0.0/104
block in log quick on gif0 from ::0.0.0.0/96 to any
block in log quick on gif0 from any to ::0.0.0.0/96
# Disallow packets to malicious 6to4 prefix.
block in log quick on gif0 from 2002:e000::/20 to any
block in log quick on gif0 from any to 2002:e000::/20
block in log quick on gif0 from 2002:7f00::/24 to any
block in log quick on gif0 from any to 2002:7f00::/24
block in log quick on gif0 from 2002:0000::/24 to any
block in log quick on gif0 from any to 2002:0000::/24
block in log quick on gif0 from 2002:ff00::/24 to any
block in log quick on gif0 from any to 2002:ff00::/24
block in log quick on gif0 from 2002:0a00::/24 to any
block in log quick on gif0 from any to 2002:0a00::/24
block in log quick on gif0 from 2002:ac10::/28 to any
block in log quick on gif0 from any to 2002:ac10::/28
block in log quick on gif0 from 2002:c0a8::/32 to any
block in log quick on gif0 from any to 2002:c0a8::/32
block in log quick on gif0 from ff05::/16 to any
block in log quick on gif0 from any to ff05::/16
# Block TCP packets that do not mark the start of a connection
skip 1 in proto tcp all flags S/SAFR
block in log quick proto tcp all
#---------------------------------------------------------------------------
# group head 10100 - LAN interface
#---------------------------------------------------------------------------
block in log quick on vr0 all head 10100
# let out anything from the firewall host itself and decrypted IPsec traffic
pass out quick on vr0 all keep state
#---------------------------------------------------------------------------
# group head 10200 - WAN interface
#---------------------------------------------------------------------------
block in log quick on gif0 all head 10200
# let out anything from the firewall host itself and decrypted IPsec traffic
pass out quick on gif0 all keep state
#---------------------------------------------------------------------------
# group head 10300 - opt1 interface
#---------------------------------------------------------------------------
block in log quick on fxp1 all head 10300
# let out anything from the firewall host itself and decrypted IPsec traffic
pass out quick on fxp1 all keep state
# make sure the user cannot lock himself out of the webGUI
pass in quick from 1234:5678:5c1:0:0:0:0:0/64 to 1234:5678:5c1::1 keep state group 10100
# User-defined rules follow
pass in log first quick proto ipv6-frag from any to any keep state keep frags group 10200
pass in quick proto ipv6-icmp from any to any keep state group 10200
pass in quick proto tcp/udp from any to any port >= 1050 keep state keep frags group 10200
pass in log first quick proto tcp/udp from any to any port <= 1024 keep state group 10300
pass in log first quick proto ipv6-icmp from any to any icmp-type 128 keep state group 10300
pass in quick proto ipv6-icmp from any to any icmp-type 129 keep state group 10300
pass in quick proto ipv6-frag from any to any keep state keep frags group 10100
pass in quick from any to any keep state keep frags group 10100
#---------------------------------------------------------------------------
# default rules (just to be sure)
#---------------------------------------------------------------------------
block in log quick all
block out log quick all
I think the user defined rules should allow pretty much anything in this config.