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I recently started using Filevault 2 to encrypt my hard drive. I read that due to security vulnerabilities, it was recommended to change the sleep settings via

sudo pmset -a destroyfvkeyonstandby 1 hibernatemode 25

This is all good and everything, but I think it's messing with some of my apps permissions upon waking the computer from hibernating? I've noticed at minimum that JiTouch and Cloudapp stop functioning correctly- jitouch completely, and cloudapp stops autouploading screenshots. It's fixed by quitting the apps and reopening, but that's kind of a hassle to do every time I open my Macbook.

Is there a way to tweak settings so apps keep their same permission set after waking?

I'm running Mountain Lion.

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