I haven't had time to read it all yet (it is sort of long and technical), but a new model by Grossberg and Seidman purports to explain how normal cognitive processes go wrong in autism -- a pretty tall order but it looks like they deliver. Here is a description from the press release:

A new model of the brain developed by Dr. Stephen Grossberg, professor and chairman of the Department of Cognitive and Neural Systems at Boston University, and Dr. Don Seidman, a pediatrician with the DuPage Medical Group in Elmhurst, IL, sheds light on the triggers of behaviors commonly associated with autism. The paper, "Neural Dynamics of Autistic Behaviors: Cognitive, Emotional, and Timing Substrates," appears in the July issue of the journal Psychological Review, published by the American Psychological Association.

"Autism involves multiple genes and correspondingly, people with autism are known to have multiple cognitive, emotional, and motor symptoms - such as impaired development of speech and difficulty expressing emotions," said Dr. Grossberg. "The iSTART model describes the various brain mechanisms that underlie autism and how they may give rise to the symptoms of the condition."

iSTART, which stands for Imbalanced Spectrally Timed Adaptive Resonance Theory, is derived from the earlier START model developed by Grossberg to explain how the brain controls normal behaviors. The new model describes how brain mechanisms that control normal emotional, timing, and motor processes may become imbalanced and lead to symptoms of autism. START and its imbalanced version iSTART are a combination of three models, each one of which tries to explain fundamental issues about human learning and behavior.

A full description of the model is available here.