Slowly gaining weight. on thyroid. atkins on the treadmill every night. i am extremely stressed at this time... could this be the problem?

Yes: If you have not had your thyroid levels checked recently, could be from that. Chronic stress tells the body to store fat--theoretically as a survival response, however our diets are much more substantial and fat-laden now than centuries ago, so we are overly efficient at it and can have weight gain. Consider seeing a counselor / therapist to help you better manage your stress.

If you are: Biochemically euthyroid (meaning your blood work shows normal thyroid levels), you should calculate your basal energy expenditure (bee) and subtract 500kcal from that number to have a goal number of calories to eat per day. Stress can certainly cause behaviors to make it more difficult to loose weight and even gain it (decreased exercise, increased eating).