I've had that and it was real bad. The pain was really bad. My left ear and eye was in agony. Turns out a nerve that goes into your brain is located there and I'd pinched it doing squats some how. I think I drove my head back as I came up.
Be careful with your neck when doing heavy lifts. Sometimes when I'm doing heavy bench I turn my head when it gets real hard, I'm not sure why but my training partner always mentions it, even when I don't think I've done it. Let it rest or lighten your load a bit.

Id watch what your doing bro I was getting pains like that when I was doing shrugs on the Calve raise machine (I know stupid of me) well I paid for it I crushed a disc in my neck just at the area your talking about The c2/c3 joint I don't want to scare you bro but I just started traing about 2 months ago and that happened in jan 2008 I've had a bad time with endless hospital visits neurologists are my new best friends. The throbbing in my case was either the muscle or the disc pushing against the nerve but this was me it maybe different for you. I started my first cycle back about 4 weeks ago now and it's great to get back but it's been a long road so just be careful dude 

Yeah, I know exactly what you're talking about. It used to happen to me during leg presses, bench, etc. It happens when you're going heavy and push your flexed head/neck up against the back/bench. It'll go away in several days, just be cognizant of your neck- especially during lifts when you have your back to something.