9 yr old with arachnoid cyst

My son is 9.  He has a history of seizures.  They started when he was 18 months old.  MRI's revealed a only a small vein abnormality.  The seizures were managed.  They stopped when he was six years old.  He has not taken any medication in 2 yrs.  A few months ago he started having headaches.  Five or six a month.  For the last six weeks he has had a headache daily.  Last Thursday at school, his teacher reported that he began to present a "flat affect", was staring as in a gaze, not participating or talking as he had been earlier that morning.  The school nurse was called.  She noticed that his pupils were uneven.  Left :  3-4 mm and reactive to light.  Right: 2 mm  nonreactive to light.  The nurse said that he then began holding his head and complained that his head was killing him.   I took him to have a CT scan.  They found something and scheduled an MRI.  They say it is a Subarachnoid cyst (18mmx17mm) on the back of his brain.  (near the bottom).   His headaches seem to come and go.  He woke up this morning at 4am and asked me to rub his head.  He also has been very emotional.  Cries at the drop of a hat and seems to have developed a bad temper. One Neurosurgeon (when he viewed the MRI) stated that the cyst was causing no problems and was harmless.  Another (whom we are seeing on Thursday) seemed to think it needed to be looked into.  
I am very worried.  It does not make sense to me that this could just be a coincidence.  My son is miserable.  What should we do?