I don't know for certain but it's a problem I used to have. It turns out (for me) that when I was focusing with my eyes closed I had a tendency to strain my eyes and sometimes even go cross eyed, but because my eyes were closed I didn't realize. I would suggest relaxing your eyes more and if that doesn't work just try what your doing with your eyes open. With practice you can visualize things with your eyes open.
What Freya says is a good possibility, however it may also be related to the entity you are working with in your summonings. I didn't have it happen to myself but some friends have told me that certain entities make your eyes hurt when you try to summon or work with them.