Is there an app embedding the Flash player?
Google Chrome comes with its own instance of Flash that runs only when it needs it and only within the scope of Chrome. I have uninstalled Flash from all my Macs and simply turn to Chrome when I really need Flash for something.
Google chrome both includes and updates it's own Flash plugin. You can also setup a command key shortcut for opening your current safari page into Chrome for the instances when you actually need Flash. See here for more info.