I too have been frustrated with the "cannot location \Windows\System32\Winload.exe" problem. I have been posting about it on the Vista Chat and Support Forum.

Anyways, I found the solution to my problem was that the second harddrive that I was installing Vista to was not in my BIOS bootable device list. Even though the bootloader is on the primary drive (C, Vista requires that its system drive (D: in my case) also be listed in the BIOS boot device list.

See my post and reply on the Vista Chat and Support Forum:
http://www.pronetworks.org/forum/viewtopic.php?t=86031

I suggested in a comment on that thread that detection of this error condition would be a great additional feature for Vista Boot Pro. It certainly would have saved me hours of messing around with multiple installs if I had known the first install I did was probably just fine... I just needed to add the drive to the BIOS boot list. Doh!