Running app for the first time NOT

Suddenly I get this message for some of my Applescript apps I have been using for years,
"You are opening the application “name.app” for the first time. Are you sure you want to open this application?"
Even after saying yes and running it the message persists every time. I have verified using the terminal that the quarantine flag is not set for the app.
Any thoughts on this? Better, any solutions?

Check your Gatekeeper settings.
System Preferences>Security & Privacy>General. 

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