The Flynn effect refers to the tendency over the last century or so for IQ scores to increase each generation by a few points.
There is no link between vaccination and autism. It is pseudo-scientific myth, which has dangerous consequences for public health. see discussion here.
I'm no expert in autism research, but in general, children with autism have lower IQ. I'm also not entirely clear how much the increasing rate of autism is a diagnostic change versus real change in prevalence (but I'll leave that to someone else). If there was a change, in real prevalence, then it would be an interesting question as to what might be causing it. One explanation that seems more plausible to me is that parental age is correlated with autism rates and that has certainly been increasing in the developed world. But this is not my area of expertise, so I'm not trying to present a definitive answer.
There are many plausible explanations for the Flynn effect related to societal level changes in nutrition, health, education, technology, parenting practices, educational strategies, screening of foetuses, and so forth. It's also interesting to ponder how much the change is related to the latent trait of intelligence, and how much is related to test taking skill. In some respects we are seeing similar societal level changes in height and life expectancy. Presumably, a whole range of societal changes could be culminating in what we see in terms of group-level IQ change.
Declines in the rate of intergenerational increases in IQ in particular subgroups may be related to some form asymptotic process. I.e., there is a point at which further IQ gains become more difficult to achieve for a society. In contrast, as social groups move from extreme disadvantage to less disadvantage, the gains may be quite noticeable. For example, I've read that the gap between black and white IQ scores in the United States has been reduced in recent years (based on greater inter-generational increases in IQ for blacks than for whites). And this in some sense speak to what the focus is on gain scores. Even if one social group has poorer environmental conditions (health, education, nutrition, etc.) than another, if the relative improvement in those conditions over a generation or two has been greater, we might still expect a greater gain.