You are certainly not alone! This is something that has gone on for a few years ago on Virgin Media and no one has really got anywhere with finding out why the performance of 6in4 is really bad specifically on Virgin Media. Like you have found, when you are fortunate enough to have another internet connection or server hosted somewhere with equal or better speed, it is pretty obvious something weird is going on in their network.
The only formal response I have seen was on their community forums where an official forum staff (employee) basically said they were not traffic shaping 6in4, but I’m not convinced. Equally they are not network engineers and getting a line of communication to that side of the company is nearly impossible.
All speed tests, download tests all top out at around a max of 20 Mbps. I’ve not seen anyone able to exceed around 20 Mbps on 6in4 when the tunnel terminates on a VM connection.
Someone else more recently tested encapsulating 6in4 over VPN (UDP) and the performance was fine. So it potentially indicates 6in4 is being treated specifically by something in the network which is degrading it’s performance. It’s slightly annoying as all evidence says they are doing something, but Virgin Media won’t acknowledge it. Equally they won’t deploy native IPv6 either, although if it’s the DS-Lite implementation, I don’t want it!