Are you behind a nat? Is your router passing protocol 41?
i'm behind a nat and protocol 41 isn't a problem. i have 2 OS's: ubuntu and win xp. in ubuntu everything works perfectly fine, with these settings.
ifconfig sit0 up
ifconfig sit0 inet6 tunnel ::216.66.80.30
ifconfig sit1 up mtu 1400
ifconfig sit1 inet6 add 2001:470:1f0a:815::2/64
route -A inet6 add ::/0 dev sit1