Ok.. I have this problem, but mine seems to be a little different.
I want to remove an old hard drive and upgrade it... this drive use to contain my windows xp install, but that wasn't even on this computer, and all the drives were wiped before installing Windows 7.
However the drive I want to remove is in the Channel 1 Primary position.
When I tell the computer to boot from this old drive, now empty except for the bootmgr... it works fine.
I copied the bootmgr and boot directory to my Windows 7 drive, ran easybcd... and rebooted... NTLDR is missing
I inserted my Windows 7 dvd and booted... start-up repair detected a problem... but said it could not fix it, Directory was not found
Manually fixing using bootrec... fixmbr and fixboot work, but rebuildbcd says Directory not found.
The Windows installation does not show up in the previous version window in the install CD... the drive does not even show up in the install cd... and this is the drive I installed to with this cd about 2 months ago.
However while using the CD, I can open dos prompt and see everything on all drives.
After all this I can still just reattach my old drive and boot just fine, but I really want to get rid of the old drive, it's an 8 year old 250GB SATA1 drive... I have a 1.5TB SATA3 drive to replace it....
If anyone can think of something else that I haven't tried... please let me know... and don't tell me to press F8