The one time that we noticed Xavier having a problem with dark circles under his eyes was when he was exposed to milk as he has an allergy to dairy. Is your son sensitive to any foods? Because our boys are on steriods they would prevent an allergic reaction from occuring, but the dark circles under the eyes can be an indication of constant exposure. I have a friend whose son (non DMD) had egg and milk allergy as a baby, had outgrown it and then at age 6 he started to have dark circles under his eyes and light sensitivity, also was having problems wetting the bed. It turned out his food allergies were back, along with wheat and peanuts.
Not sure if this helps you or not, but for me when I hear dark circles under kids eyes and sensitivity I immediatly think food allergy due to life experience.