My daughter with SWCAH actually started complaining of stomach pain about the same age.  Since I questioned whether or not it could be related to her medication, our ped ordered a sonogram of the stomach and pelvic area.  The test was negative, but the ped reccommended giving her meds in the am with food.  The problem was, my daughter didn’t want to eat breakfast most days.  So I got her in the habit of having breakfast, then taking her pills after, which seemed to help.  Now, At age 9, she just takes her Cortef and Florinef with milk, then eats, and doesn’t have any problem.  Also, at 6, she was going through alot of emotions, didn’t want to go to school, etc., so it may have been that too.  Good luck.