In the comments there is a handy tip:

"Third, restoring a bootable windows to a different partition is slightly painful. Having a bootable XP/W2K cd will help a lot - fixboot and bootcfg but you can help yourself by pulling extra lines for partitions 1,2,3,4 in the boot.ini before starting!"

By which they mean, a normal boot.ini will look something like this:

[boot loader]
timeout=30
default=multi(0)disk(0)rdisk(0)partition(1)\WINDOWS
[operating systems]
multi(0)disk(0)rdisk(0)partition(1)\WINDOWS="Microsoft Windows XP Professional" /fastdetect

Before cloning, change it to:

[boot loader]
timeout=30
default=multi(0)disk(0)rdisk(0)partition(1)\WINDOWS
[operating systems]
multi(0)disk(0)rdisk(0)partition(1)\WINDOWS="Microsoft Windows XP Professional" /fastdetect
multi(0)disk(0)rdisk(0)partition(2)\WINDOWS="Microsoft Windows XP Professional 2" /fastdetect
multi(0)disk(0)rdisk(0)partition(3)\WINDOWS="Microsoft Windows XP Professional 3" /fastdetect
multi(0)disk(0)rdisk(0)partition(4)\WINDOWS="Microsoft Windows XP Professional 4" /fastdetect

Which means that if you restore to a different partition you can pick the correct one to boot from from the startup menu after you've cloned.

http://support.microsoft.com/kb/289022