System Unstable after 10.8.3 install w/ Thunderbolt Display

I installed 10.8.3 on a MacBook Pro last week; system has a Thundebolt Display used as primary monitor, though both monitors are on and in use.
Randomly, but not less than 3-5 times per day, all the windows on the machine will freeze. displays stop updating, windows stop moving when you try to drage them, KB doesn't put keystrokes on the screen. Seems locked up.
Careful observation shows that the system consumes mouse inputs perhaps one every 15-30 seconds. If I click on a sequence of things, and then stop and wait, the system does, indeed, respond to the mouse inputs verrryyyy sloooooowwwwllly.
Only way out, at first, seemed to be a hard power down.
I realized this week that if I immediately disconnect the thunderbolt cable that connects the macbook to the display, and wait a few minutes, the windows come back alive and the situaiton resolves on the laptop (now, without the display attached). I have not had the problem happen on the laptop alone.
frequency is increased by having activity on both monitors (laptop and thunderbolt)
frequency is increased by using webcam on Thunderbolt display (with Skype, for example)
using parallels seems to increase the frequency
I've used this system rouintely for a couple of years; this upgrade has essentially rendered it unusable

Please read this whole message before doing anything.
This procedure is a diagnostic test. It’s unlikely to solve your problem. Don’t be disappointed when you find that nothing has changed after you complete it.
The purpose of the test is to determine whether the problem is caused by third-party software that loads automatically at startup or login, or by a peripheral device.
Disconnect all wired peripherals except those needed for the test, and remove all aftermarket expansion cards. Boot in safe mode and log in to the account with the problem. Note: If FileVault is enabled, or if a firmware password is set, or if the boot volume is a software RAID, you can’t do this. Post for further instructions.
Safe mode is much slower to boot and run than normal, and some things won’t work at all, including wireless networking on certain Macs. The next normal boot may also be somewhat slow.
The login screen appears even if you usually log in automatically. You must know your login password in order to log in. If you’ve forgotten the password, you will need to reset it before you begin. Test while in safe mode. Same problem? After testing, reboot as usual (i.e., not in safe mode) and verify that you still have the problem. Post the results of the test.

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