This is an old post, H1N1 hence the vaccine wasn't even out yet.
did he receive H1N1 vaccination before these symptoms? my toddler has the same symptoms ever since he took the vaccination
He may have blepharospasm. I have that myself and it is very annoying and very uncomfortable. I have had it my whole life. When you go to the doctor, mention blepharospasm.
Have you had him at the Optometrist? They have a special way of checking there vision even at this young age. He may be straining his eyes therefore his eyes are getting tired and blinking for relief. My son does this so I do have to put in the saline drops but he also has glasses. Good Luck.