Closed queries re-open when connecting to DB using MySQL Workbench
I thought this was some kind of auto-save feature from Amazon EC2 instance or some kind of bug, but nope my bad.
I found bug report and at the bottom of the page this is the answer:


  Andres Giordano:
  This is not a bug!!! You have to go to Edit --> Preferences --> General --> SQL Editor (panel) and uncheck "Save snapshot of open editor...."


That's the correct answer. Once this option is disabled, no more queries are stored and re open.
I hope this tip is useful for somebody. Greetings!