I figured it out. The problem is with VB code and not MediaLab. Basically, at the end of the presentation the message "would you like to save changes" appeared because - I assume - all my defined variables in VB were not set to their initial state. Basically, I have just added a sub that 'initializes' all my variables to their initial state, and then I add a line to close the application in the same sub (e.g., ActivePresentation.Quit).