Sites for 'automatic' learning in the brain are regions like the cerebellum, that help coordinate information coming in from the senses, motor plans, and adjustments that the body has to make when its doing something. Traditionally, brain regions like cerebellum have been relatively neglected by neuroscience research (conscious regions have attracted more attention), but now the cerebellum finds itself at the center of attention of some of the most critical childhood behavioral syndromes of our time: ADHD, autism, and sensory integration dysfunction.
In fact, cerebellar abnormalities are now recognized to be the dominant site for inflammation in autism (see post above), but it is also the site for abnormalities in ADHD, and from injuries due to birth injury, prematurity, or low birthweight.
Part of the reason that cerebellar problems may present with behavioral difficulties is that the cerebellum directly connects with the hypothalamus. It is a relatively primitive part of the brain that can activate the autonomic system direcly, and affect mood, arousal, and attention. Also because most of the cerebellum's actions are not under directly conscious control, some of these other activations may occur 'without thinking'.
Unfortunately the excellent Dysmetria of Thought article below is not yet available for free access. But in the coming year, there will probably be many more interesting studies about what makes 'automatic learning' difficult in ADHD, Autism, and SI.
Dysmetria of Thought
Neuroinflammation in Autism
Spatial Attention Cerebellum
Cerebellum ADHD Abstract