A disk in a workmate's computer failed recently, and when restoring the backup, we had issues getting the second partition to boot. We were able to get the OS to load only as far as the second loading screen (the blue screen with the scrolling orange/blue animation at the bottom, not the black screen with the scrolling green animation at the bottom), at which point the scrolling animation would freeze (although the keyboard and mouse were responsive).
We have tracked it down to the drive letters being changed, and can reproduce the problem on a working machine by changing the drive letter of the boot drive as outlined in the Microsoft Knowledge Base article 223188.
As an aside, partitions above the 1024 cylinder boundary are not bootable. For a Windows partition to be bootable, the following files must reside before the 1024 cylinder boundary:
We resolved our problem by not dual-booting (the second partition was only necessary for running Norton Ghost under a 32 bit environment, but more recent versions will run under a 64 bit OS), however, if you have this problem, try editing the registry on the new partition to reflect what the drive letter should actually be.