I had the same problem - late afternoon headaches, tiredness. It was a colleague who took one look at how close I sat to the monitor to tell me to get my eyesight checked. Diagnosis: long-sighted in one eye, short-sighted in the other, which caused quite significant muscle strain while my eyes constantly fought eachother for focus, causing headaches and tiredness. Prescription goggles and the problems vanished.

Get your eyes checked, at best you get told you have 20/20 vision and you're mad, and to drink more coffee. At worst you're in line for glasses