Macbook shutdown hanging - dock stays open

Hey, my first post (excuse the username, I made this account years ago...).
I've had a problem shutting down my new MBP Retina 13'' recently. Often (not every time however), when I go to shutdown the computer (Apple > Shut down > shut down), the computer appears to be shutting down normally (the menu bar and desktop icons disappear), but then the dock stays open, and does not shut down. I've waited and waited but it doesn't shut down. To get it to finally shut down, each time this happens, I have to hold the shutdown button and select shutdown again, and then after a few seconds shutdown occurs normally.
I spoke to Applecare on the phone, they told me to perform a safe boot and then it should be okay, and it was for a while until it started again. I went into an Apple Store today, and they said it's 99% likely that it's just something like an app or process causing it to hang. The guy suggested to toggle my login items on and off and see if that fixes it, which it didn't (I only have 2, Dropbox and Caffeine).
Can anyone relate or have any ways to fix this? It's not that bad, but just annoying enough to bother me. Thanks!

Reset SMC. http://support.apple.com/kb/HT3964
Choose the method for:
"Resetting SMC on portables with a battery you should not remove on your own".
Start up in Safe Mode. http://support.apple.com/en-us/HT1564
Best.

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