Upstairs Story Not Cooling Despite Working AC?
It looks like the air handlers are both in the basement.  There will be a fairly significant friction loss due to the added distance of the second story air ducts.  If the ducts weren't carefully sized and balanced from the beginning, this could impede the airflow.  

Another factor could be the return air.  If the upper story does not have its own return air, then the returns will be sucking air from upstairs down to the lower floors when the system is on.