You can always fix it with the Windows XP CD and fixmbr and fixboot command.
I also forgot to mention another great tool for cloning, it's CLONEZILLA!!!
Get it here Clonezilla
These tools are free and good to have around. I suggest using cloning for boot partition so you don't have to fix the MBR. Use copy from Gparted if you want to just quickly backup data on a regular partition to another HD.
*Edit* Just found out Gparted will not work if you try to copy a boot partition to another HD and boot off it. It only copy data, not boot sectors. Only way is to use fixmbr and fixboot.
Another way is to use dd. Boot into Gparted and close it to the terminal and use the command
dd if=/dev/hda of=/dev/hdb bs=512 count=1
Where hda is the IDE hard drive you want to copy from and hdb is the IDE hard drive you want to copy to. It should copy the first 512byte (MBR) to the other HD.
hda = IDE hard drive
sda = SATA/SCSI
so for SATA/SCSI, should be
dd if=/dev/sda of=/dev/sdb bs=512 count=1
hda1 = First partition of IDE HD
sda1 = first partition of SATA/SCSI.
anything from #5 are logical drives
You get the point.