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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.

"Coda 2" is an application downloaded fro the Internet. Are you sure you want to open it? Safari downloaded this file on August 29, 2012

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?

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And this is every time you launch these apps even after confirming the dialog? I'd try Repair Disk Permissions first in Disk Utility. –  Gerry Sep 1 '12 at 8:37
    
@Gerry just tried that and found some permissions errors but unfortunately the problem still persists :( –  blogjunkie Sep 1 '12 at 9:12
    
Have you tried rebuilding the Launch Services database? –  Lauri Ranta Sep 1 '12 at 9:16
    
Tried that and I got: -bash: /System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/LaunchSe‌​rvices.framework/Versions/A/Support/lsregister: No such file or directory Is that the correct command? I'd appreciate it if you could repost in pastebin.com –  blogjunkie Sep 1 '12 at 9:20
    
I edited the comment a few minutes after sending it. Stack Exchange inserts ZERO-WIDTH NON-JOINER characters in the middle of long strings without spaces. –  Lauri Ranta Sep 1 '12 at 11:44
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2 Answers

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.

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Thanks! That was getting annoying---for me it was Adium –  Dolan Antenucci Mar 30 '13 at 10:23
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If other applications keep showing the dialogs, you could also try disabling the quarantine warnings completely with defaults write com.apple.LaunchServices LSQuarantine -bool false. It also disables the warnings shown by Gatekeeper even if it was enabled in System Preferences.

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