This is the response from Intel Engineering:
We found that Bios 0025 works but Bios 0028 introduces some changes (and fixes). However, we need to load the Seagate Thunderbolt Windows* driver.
We have it working for now on Bios 0036 with Seagate goflex (STAE121). Please try this driver and reboot a couple times: http://www.seagate.com/support/external-hard-drives/portable-hard-drives/goflex/thunderboltwin-master-dl/
On the first boot the yellow bang was still there, but it detected and once the system is rebooted the drive is accessible.
I really appreciate you looking into this issue. Unfortunately, I still am having trouble getting the STAE128 to start under Windows 7 x64. I already have flashed the mb to Bios 36. I downloaded and installed the drivers that you suggested. They appear to have installed okay. I have the STAE128 with drive attached to the thunderbolt port with an apple thunderbolt cable. I have rebooted four or five times and the Asmedia 106x SATA Controller is still yellow in device manager with the error "This device cannot find enough free resources that it can use. (Code 12)" Could the STAE128 have different firmware than the older STAE121 that makes a difference? Unfortunately, I don't think that I can flash the Seagate adapter without being able to connect to it.
Thanks again for any help that you may provide. I really need to get storage thru the thunderbolt port working because my mSATA boot drive is too small for my design.
this might be a windows, not NUC, problem. i have a "different" OS installed on my NUC, and after booting from a usb stick, i have no problem accessing my thunderbolt drive using a seagate STAE129 adapter (the 3.5 inch drive model). further, using Clover bootloader in non-UEFI mode on a USB stick, my TB drive shows as a bootable option, so i boot directly from the TB drive.
UNFORTUNATELY, intel chose not to enable native booting from a thunderbolt drive, for who-knows-what reason. maybe we'll be lucky and that will be added to a future bios version. other computers/mobos with thunderbolt ports do in fact enable booting from thunderbolt drives. not sure what was behind intel's decision to not enable it.
note: i don't have any SSD at all. i use my NUC as a media center computer, so i knew i needed a very large HD for all my video content. i'm using a 2TB SATA III HD in the seagate thunderbolt dock. it is plenty fast!
I just installed Windows 8 and my thunderbolt drive came online "plug and play" without any drivers or effort on my part. In general my impression is that the NUC plays much nicer with Windows 8. Life is good!