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I'm on Mountain Lion. Every time I double-click on a pdfd (pdf bundle) document, I get the alert saying that I'm opening Skim for the first time (which is, of course, false).

I've completely disabled the quarantine system. I also tried to reset the LaunchServices database.

How can I fix this?

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Are you running Skim from its mounted dmg? – lhf Aug 14 '12 at 12:07
No: it's in the Applications folder – user732274 Aug 14 '12 at 12:08
Another question like this was solved with sudo xattr -d /Applications/$ – user495470 Sep 9 '12 at 12:15
up vote 2 down vote accepted

Solved: I had to trash Skim, rebuild the LaunchServices database, restore Skim and rebuild the database once again.

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