I see what you mean. I think though that some differences are: the vaccine/autism movement began out of a single study that was later retracted that showed a connection. The CCSVI movement began out of studies by Zamboni but his initial finding (that CCSVI is much higher is m.s. patients than in the normal population) has been replicated. The other thing is that, unlike vaccines and autism, the CCSVI/m.s. connection appears to be a simpler mechanical one...not sure if that's the right wording for what I mean...it's that it should be relatively to test and prove one way or the other.
"However, the truth in science ultimately emerges, although sometimes it takes a very long time," Arthur Silverstein, Autoimmunity: A History of the Early Struggle for Recognition