That's a normal alert box that you should get the first time you open an app that you have downloaded, and added to your system.
It's something that you should expect to see - the first time.
Click the OK box, because you know where the app came from, and you can assume that it is "safe" (correct?)
Do you get the same message when opening another app, even though you are certain that you have already opened that same app before?
Ah, OK, I did miss that little detail.
I was referring to what I call the Quarantine release window. Yours is the similar URI handling release dialog.
But, here's a fix: http://apple.stackexchange.com/ques...pening-application-for-the-first-time-dialogs
I would try that same terminal command again.The warnings should pop up once for each application again after that, then be gone for good. If they keep coming, something is resetting the database on its own (a clue would be that the default browser / mail app / RSS app / FTP app you set keep resetting to the Apple provided ones).