Thanks for the extra questions.
It is not a BIOS or a boot.ini thing. I get a blue screen when it tries to load the raid controller drivers, which is during the famous
Loading Windows 2000
........
Its a bit like this, during a blank install of Win2k if I don't press F6 to install the additional drivers the computer cannot see the disks.
So in my situation I have a working Win2k OS installed, all raid arrays are setup the same as original server (note: very simple config).
The working system is using the correct drivers that I gave it during install. By me performing a complete recovery from another machine old server it overides the entire new servers setup. So the registry has references to the old raid controller drivers.
Hence after a reboot when it get to the part of loading the drivers in order to continue with loading the OS it fails because it tries to use an old controller driver. The disks therefore cannot be seen by the OS and it does not boot.
Microsoft recomend installing the new raid controller drivers on the existing server before performing this type of operation. This way the server should still boot it will just get an error when it tries to load the old raid driver.