New research suggests autism starts in 2nd or 3rd trimester, resulting from "overwiring" of brains.

I found this article through a friend of mine who's associated with the Autism Science Foundation.

These results provide insight into the origin of autism. During the second trimester of pregnancy, the precursors to neurons in the brain divide furiously. Then they almost all stop, well before birth. When the brain gets bigger after delivery, all that is happening is that the individual neurons are growing and sprouting branches. The only time autistic children can get their extra neurons, in other words, is while they are in the womb. “We established a time zone,” Courchesne says.

That time zone rules out the old bad-mothering theory of autism, and also the notion that vaccines trigger autism in toddlers. Courchesne suspects that fetal brains become autistic due to a combination of genetic and environmental influences that strike during the second and possibly third trimesters, just as neurons are dividing. It may be no coincidence that many of the genes thought to increase the risk of autism are also involved in the division of cells. It’s possible that an environmental influence—perhaps a virus—can trigger these genes to produce too many neurons.

When autistic children are born, Courchesne’s research suggests, they have an abundance of neurons jammed into an average-size brain. Over the first few years, the neurons get bigger and sprout thousands of branches to join other neurons. The extra neurons in the autistic brain probably send out a vast number of extra connections to other neurons. This overwiring may interfere with normal development of language and social behavior in young children. It would also explain the excess brain size seen in the MRI scans.

http://discovermagazine.com/2012/mar/07-the-brain-troublesome-bloom-autism/

While it's an imperfect analogy, the human brain is in a lot of ways like a large, bioelectric computer processor. Electrical impulses flow through dedicated pathways, paths that need to be kept separate in order for the brain to work using it's original specifications.

Essentially what's being described here in this article is that due to the overcrowding of neurons, the brain is short circuiting, like if you just started randomly crossing wires in a computer. The difference is, a human brain is also equipped to try and adapt to problems, including malfunctioning areas or even physical damage to brain tissue. The brain, unable to operate on the original pattern, basically attempts to rewire itself on the fly, resulting in a variety of degrees of functionality.