Generally when you take medicine with high acidity food, like coffee, it will break down your medicine prematurely - you won't get as strong as an effect. I had to stop taking my Vyvanse with orange juice because it basically nullified the medicine.
Talk to your doctor. I had chronic headaches that I found out were related to low blood pressure and dehydration. Drinking water instead of diuretics, like coffee, immensely helped me.