The pop up to update Flash comes from several sources:
1. You have Flash installed and a video starts that triggers the Flash application itself to warn that the version you have is old. You get rid of this by completely uninstalling Flash, removing it from your browsers and then rebooting to a clean no-Flash system.
2. Bad dudes want to get you to go to their site to get what you think is Flash but which is actually some form of Malware. Ghostery should block those, if you have it turned on and blocking all the nasties. Did you do the "turn on" step for Ghostery? (Click on the ghost icon in Safari, or whatever browser you use, and click either Default or Custom)
3. Sometimes a fragment of Flash gets left behind if the installation was not done correctly. You may need to manually check for anything from Adobe and eliminate it. You can use EasyFind or Find Any File to search for all things Adobe and get rid of it. (That assumes you don't have any other Adobe products installed. If you do, you'll have to be careful not to eliminate something you actually need for that other product.)
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Also, is there one specific website that triggers the popup all the time? Maybe it's embedded there. Not all websites are "good" websites.