I recently created a t1.micro instance running Ubuntu Linux. I then used that instance to create an image that would allow me to clone more instances. Installed LAMP and PHPMyAdmin on the parent instance so naturally, the cloned instance took on those properties as well. It's my understanding that each instance has it's own LAMP server that is autonomous of all other instances' LAMP servers. So, why is it that when a query is executed on the parent instance that it also executes on the cloned instance?
You must be connecting to a hostname rather than localhost (a mysql instance hosted on the local server), if mysql commands affect the same mysql instance when initiated from different servers. Post the config of ~/.my.cnf or else elaborate on how you are actually connecting to the mysql instance from either of the ec2 instances.