Why do I have repeated "Are you sure you want to open it?" messages when launching applications? My Security settings are set to "Mac App Store and identified developers". I'm still getting this problem though I've allowed the app to run more than once as an Administrator. Specific apps that are experiencing this problem are Coda 2 by Panic, PDFpenPro by Smile Software, and Firefox.



Panic and Smile Software are identified developers if I'm not mistaken. And Transmit by Panic opens fine without these warnings.

Any idea why this is the case?
Solved the problem! The quarantine metadata was not clearing correctly for some reason. I fixed this by doing:

sudo xattr -d com.apple.quarantine /Applications/Coda\ 2.app


Big thanks to Thomas Reed in the Apple discussion forums - Link to answer.