First of all, you are talking about 6to4, as such, even though next I will ask for a traceroute, it won't help much as packets might be pulled to the left and right and other unknown directions on both IPv4 and IPv6, both of which might be anycasted, thus debugging 6to4 is nearly impossible unless one would have access to every single hop along the route, which most very likely is not the case. Which exact host are you trying to reach? www.sixxs.net and the IPv6gate too are hosted on a cluster of different servers at different ISPs, as such that might make it even more difficult to debug, but a traceroute to each might already help a bit. That could quite well be an MTU issue. For 6to4 this is always 1280. That looks more or less fine, nothing much one can state about those details. Other details are way more important though. Can't do much about a closed box, as one can't even look inside it.... The only thing you could do, but might be far from ideal, is to use another host for terminating the tunnel and distribute a subnet from there.

Out of curiosity; what limitation is that? Both my Extreme-boxes has options for a IPv6-over-IPv4 tunnel. I've never tested them though, but can't think of any reason it /shouldn't/ work.