Thanks for this interesting question. While there may be some good explanation, it is likely that seeing what you are trying to describe would help to make this easier to understand and explain. That is why I recommend speaking with your doctor
about your question. I'll try with the information that I have. The nerves in your brain are wired to the rest of your body, and your body has nerves that then interact with the muscles. There are both efferent (nerves that go to the body) and afferent (nerves that go to the brain) nerves in the nervous system. These different branches interact with each other and are interacted upon both in the central nervous system (brain and spine) as well as in the synapses (where one nerve ends and another begins, a sort of relay station where a signal can be modified, amplified, etc). There are reflex arcs that sometimes bypass the normal central nervous system control, and instead generate a muscular or other response when certain areas of nerves are affected in a certain fashion. It could be that you are experiencing some variation of a modified reflex arc, where the microscopic movement that you suppress with your itching generates a movement somewhere else, but it is not clear without more information. Again, please speak with your doctor.