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There are many possible causes for an intermittent ache in your eye associated with photophobia. Some of them are serious, some of them are very serious and some of them are not really a problem at all. For example, you could be suffering from intermittent angle closure glaucoma, uveitis, infection or dry eyes. Without seeing you or having more information I really can't tell what it could be for sure.
I am glad you were examined by an eye care professional and nothing serious was noticed. I believe, however, that you really need to be seen by an eye doctor (MD) for a complete dilated examination. The ophthalmologist should be able to rule out many of the serious conditions that could be causing your discomfort even if you are not having the pain at the time of the exam. A complete eye exam will also check for tear film, tear gland or eyelid issues that could be contributing to your symptoms.
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