Apple has released Thunderbolt Firmware Update 1.0 for Macs that ship with the new Thunderbolt interface.
The update is currently available via Software Update on your Mac or via download.
According to Apple:
About Thunderbolt Firmware Update
This update provides Thunderbolt performance and stability fixes.
When your computer restarts a gray screen will appear with a status bar to indicate the progress of the update.
Do not disturb or shut off the power on your computer during this update.
The download is only 468KB and requires that your Mac has Mac OS X 10.6.8 installed.