Hello jadt,
Thank you for posting in the Apple Support Communities. You may want to try downloading the Thunderbolt 1.2 update directly from our site if it is not installing through software updates:
Thunderbolt Firmware Update v1.2
http://support.apple.com/kb/DL1653
If you are still not able to install the update after downloading it directly from our site, you can follow the steps in the following article:
Troubleshooting Mac OS X installation and software updates (Mac OS X v10.6 and earlier)
http://support.apple.com/kb/TS1394
This article has "Mac OS X v10.6 and earlier" listed in the title, but the steps should also work for Mac OS X v10.8 as well except for the steps where it tells you to boot to disc (with Mac OS X v10.8, you will need to use the recovery partition in place of a disc). I recommend following the steps listed under "Troubleshooting an unsuccessful installation," and skip any steps that you may have already taken.
Best,
Sheila M.