Hi Tim,
There are a couple of things I'm not clear about from your post.
1) Is this a new computer to replace an existing on that is running some equipment?
2) What size is the hard disk you are trying to copy?
Obviously the program you are using is not making and transferring an image of the boot partition. If this were so then it should boot from the restored image. As Thomas says use Dfsee
http://www.dfsee.com/ to make and restore an image file of the HD (there is a version that works with windows).
If you are replacing an old computer with a modern one then there could well be other factors involved as well that could prevent it booting so more details as to the equipment would help us to help you.
ivan