A curious interpretation of these involuntary physical motions that many report was offered on a recent retreat. U Jagara mentioned that Pa Auk Sayadaw (the Burmese master famous in the West for his jhana methods) thinks that such phenomena often result from improper perception of the breath along the lines of the wind / air element, rather than as just a subtle sensation of touch. That somehow evokes "wind" (motion) in the mind-body.
Touch, in the Abhidhamma literature, has a unique character among the 5 (physical) sense-doors, in that is consists of earth, heat, and air/wind qualitites (but not those of the water element). Touch also pervades the whole body, not only in the sense of proprioception basic to the mind's (awareness) role in helping regulate life functions, but also even touch sensation of "external" agents is in a sense an awareness of bodily reaction to the stimulus. The other 4 sense doors (vision, hearing, smell, taste) relate more directly to the external stimuli. So the touch sense is uniquely suited to meditation as secluded, internal mental work.
Jagara didn't go into a lot of detail, but indicated that the phenomenon often is the result of lack of, or improper training, rather than something wrong with the individual or meditation itself.
The elements (Maha-Dhatu) aren't that well known in Western circles, but are important meditative objects in both the Pa Auk and Mahasi Burmese traditions. After "noting" or concentration are well established, then it's used to discern how perception is made-up of (or "deconstructed" into) the various particular elemental qualities, and how the mind associates specific groupings of these micro-qualities of perception in recurrent patterns, and gives these patterns names or concepts, e.g. "tree", "pig", etc.
Maybe a combination of shaping the breath object as moving air, and the mental-physical tension of "trying", or striving builds into such involuntary, often distressing, bodily movements. It probably would take the direct (personal) help of a skilled teacher to diagnosis it more exactly, and suggest corrective action suited to the individual case. Overall, there might be an exploring the smooth, quiet, calming aspects of breath, building pleasant sensations and spreading a kind of tranquility throughout the body, which also can serve to help uncover and unwind those little tensions that most people carry around in their musculo-skeletal system unconciously most of the time.
Thanissaro Bhikkhu's recorded guided meditations (at audiodharma.org or dharmaseed.org) often focus on this kind of body-scanning for starting up meditation and building a good basis for concentration. As he puts it, first get the body into position to meditate, only then can the mind get into position to meditate. (Otherwise the mind will be distracted by bodily issues that intrude.)
