So I ran into an issue while setting up native VHD boot into a windows server 2008 r2 server, native VHD boot just wouldn’t work when I place the VHD onto my additional (bigger & faster) hard drive that is sitting on a ultrabay, If you’ve got a t61 I recommend getting one and swapping out the dvd drive with ultrabay which will allow you to add an extra drive for those VHD’s.
All my existing VHDs that is sitting on main disk works fine for native VHD boot, but the ones on Ultrabay hdd did not.
After some hrs of searching internet and pulling my hair, I figured out the reason for this was my HDD on ultrabay was excluded from the boot devices list, added it to boot devices list and it worked like a charm.
As far as setting up native VHD boot I recommend following the screencast by Keith Combs
Windows 7 VHD boot setup guideline post from Knom’s developer corner