hmm, puzzling.
I vaguely seem to remember seeing that update come through with the others yesterday when I was rebuilding my rMBP, but it all works fine for me - which isn't a lot of help to you I know.
and I don't suppose repairing permissions or resetting the nvram would fix it on yours?
I had an issue on the wife's Air recently, started up from Recovery Disk on a usb stick and repaired permissions from there.
restarted as per normal and everything's been fine since
Here's a better look...
sometimes repairing permissions internally - i.e. Disk Utility on your Mac - is not as effective as performing the procedure from an external source.
drastic solution - back up; erase and clean install, update everything then add Apps and finally pull your data across manually.
fail-safe but a tad extreme.
I'm sure someone else will come up with a simpler, effective solution for you - in fact I'm surprised no one else has weighed in as yet.
you're out of 90 day free Apple phone support I presume?
I had the same problem right after the firmware update on my MBP 15" Retina, Safari was hanging and asking for Keychain access - Mail was stuck too, incapable of accessing mailboxes.
When I saw this post I got nervous ... reinstalling!?
I just simply rebooted the machine... it's all good now - very simple fix!