Hi Dillon - I have had this same thing happen to me and I went to the Eye Doctor and was told I have dry eye which I now put drops in my eyes every day. However, I did find this article as well and suggest you make an eye appointment with an ophthalmologist right away as any type of eye pain like what you are experiencing can lead to damage to your eye. Here's an article that I found:
http://www.everydayhealth.com/visioncenter/healthyeye/specialist/behrens/sudden-eye-pain.aspx
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This is probably the atmospheric pressure in one of your sinuses increasing as you dive. Sometimes it can escape and then you do not have pain.
I'm not that familiar with diving but I'd wonder if maybe you've a predisposition to form an air bubble there which would of course expand as you're rising to the surface too rapidly. But that would only apply on your way up, not when entering or on your way down.
Else, it's sounding like you may have some sort of internal injury (dive / decompression related?), and the pain is pressure on the injured portion that's making itself known intermittently (likely to become consistent I'd suspect, especially if the injury were slowly worsening). This may be something the dive community is pretty familiar with (I'd be asking in a diving forum for other's experiences along this line).