Go back to the eye doctor and let the doctor know what is happening. I did not want to go back to my eye doctor, but my doc told me to keep coming back until they were right. He said that he can't help me unless I keep coming back and letting him know.
I recently had the same thing happen to me. I had a change in my prescription, and it just made my migraines worse. I went back to the eye doctor. He fixed my prescription by taking out the fix for astigmatism. He explained that some people cannot handle it and it causes their eye to strain and pull, even though it is the true prescription. As soon as I put the glasses on without the astigmatism fix, I could tell right away that they felt better. I don't know if that is your case, but just go back and see what your doc has to say about your eyes and glasses. My doc redid the whole test, and was really nice about the whole thing.