I have OCD about certain things. App and system updates are one of them. Unless I have a specific reason not to install an update (e.g. the Internet complaining about an update making an app, or OS buggy) then I usually go ahead and install them.
Last week, after attempting to install the MacBook Air Flash Storage Firmware Update 1.0, the update was still available on the App Store after I rebooted. Obviously this bothered me. I attempted the update at a couple of different intervals over the next few days. It still didn't work, and still my OCD was not satisfied. I complained on App.net, and within a few hours I had an answer from David Ross:
@reagan I had to turn off File Vault 2 on my boot drive, then re-encrypt after the upgrade.
If you haven't heard of FileVault before, it's an encryption option in OS X provided by Apple. I've used it for a while, and it works great. Anyway, back to the story.
I'm not exactly sure why this worked, but it did. Keep in mind that you'll need to restart after you disable File Vault 2 in System Prefs, and that after the restart it will take a few minutes for it to decrypt your boot drive. It took my mid 2012 MacBook Air about 15 minutes to decrepit.
Also, don't forget to re-enable FileVault 2 after the update is done. Not that I'm speaking from experience.