Since your child feel fine with his glasses in the first several days, it cannot be the problem of the glasses. Maybe it caused by Conjunctivitis which will also make your eyes blink frequently. You'd better take your child to a doctor and have a careful exam.
I think it has nothing to do with wearing glasses. Blinking frequently may be a sign of conjunctivitis. People with squinting eyes can also have such problem. It is better to take him to see the doctor and find out the problem.