It sounds to me like eye strain. I've had problems with that especially in the right eye, and the eye doctor thinks it's strain. I spend at least 80% of my waking hours on the computer, so it's definitely putting a strain on my eyes. I got computer glasses to use recently, and the throbbing is lessening.
Make SURE you rest your eyes right now (assuming your problem is strain). Get proper sleep (I don't and can't because of my job, which does add to the strain).