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?