[[ Im convinced its software based as it was fine up until the firmware update came out and I think through trying to get that installed its buggered it up. ]]
I had a similar problem with my own 2010 MacBook Pro, but with firewire.
One day (computer was still under warranty), the firewire stopped working. Didn't even show up in System Profiler.
I took it to the Apple Store, and got the logic board replaced under warranty. At the time, the tech guy said that it might not be just a hardware problem, but in software as well.
After about 6 months of use, I did some kind of update (I think) and --- no firewire again. By this time the computer was OUT of warranty, and I didn't really need firewire, so I just let it go.
Then, I decided to install either Lion or Mountain Lion on it (old OS was 10.6). I used a second partition, still keeping OS 10.6 on the "main" partition.
Got the installation completed, booted it up and -- suddenly, firewire was back working again. Even works on the 10.6 partition that it -wouldn't- work on previously.
All I did was install an updated version of the OS.
So
I'm guessing that at some point during the initial boot process, there was -some- software file (perhaps a kext?) that either wasn't there or was corrupted and couldn't be read at boot time. And without that software, the Mac's firewire circuitry wouldn't "activate".
Could be the same with thunderbolt.
I'm thinking that perhaps something got corrupted in firmware, that would be necessary to "be there" in an UNcorrupted state for thunderbolt to be "activated" at boot time.
Do you have an Apple Store you could take it to, to have the firmware checked out, and possibly "re-flashed"?