I am encountering a perhaps related problem with my Thunderbolt monitor on a 13" mid-2011 MacBook Air. Since having installed the security update 2013-003, both keyboard and ethernet which are both connected to the screen, sometimes won't work. The screen is always there, however. This only happens when I arrive at the office with my laptop and connect the screen. I also haven't yet found a consistent solution (it has happened only twice so far, but never before the update), but my current "method" is to restart the Mac without the monitor attached and then connect later. Of course that won't help in your case...
I will also file a bug report with Apple, hoping that it gets their attention.
I also noticed a new effect last night...
When I put the iMac to sleep, both monitors go dark and power drops down low (I have a meter).
But if I unplug my iPhone or a USB device, the iMac wakes up "a bit" although its screen remains "black", but the 2nd monitor comes on "with signal" although it too is "black display". It never falls back asleep; never loses signal. Power usage is up a bit.
There appear to be at least 20 threads regarding Thunderbolt/DisplayPort problems, so I assume Apple still have not worked out good drivers for the variety of monitors and display resolutions out there.
Generally, turning the external monitor off for 15 seconds seems to work for me, but it's a real hassle...
In my case, it's not an issue of the iMac's screen flashing blue, the iMac's screen just simply randomly turns off. I posted an update in the thread I started [ https://discussions.apple.com/message/22404953 ] where the issue seems to go away if I don't let my computer go to sleep. If I don't let the iMac go to sleep, then the screen turns off and on as it should.