I'm not certain why a simply copy/paste doesn't work but I'm guessing it has something do do with hidden files/partitions/properties/mbr/etc.
Regardless of why a straight copy and paste doesn't work there are a few methods that you can use to "clone" your hard drive. You can use backup software to create a system image. This is basically a clone of your current hard drive's status and it allows you to restore your computer to exactly that point from scratch. You could also use disc management software to clone your hard drive in the manner you're speaking of. I'm not sure if it'll work properly on a boot disc but you could try. Keep in mind that it's best to clone the hard drive using a live cd so that you're not booting off that hard drive at the moment of the clone.
More about backup software...
Personally, I don't recommend using the Windows version of backup software because I've found it's unreliable. However, many people use both third party and Windows versions of backup software and both work. The key is finding a method that is reliable for you.
I use a free program called Macrium Reflect. It's a backup software that allows you to clone any partition and save a copy. You can then use a Linux Boot Disk to restore that image to any hard drive with sufficient space. The one thing you want to make sure of in this configuration is that the boot disk works for you.
For your first test, I recommend backing up all of your information before doing anything. Once you've done this, create a system image and place it on a secondary disk. Now create your Linux Boot Disc. Boot from this disc and attempt to access your system image. If everything works properly and you can access the system image on whatever secondary disc you're using, use that image to restore your hard drive. This shouldn't take too long as long as your primary disc isn't too large. Anyway, if everything works properly then you know you have a reliable backup method. Now you can create system images on a regular basis and keep a base system image from just after you've installed your operating system and drivers
I highly recommend doing that last part. Once every few months, I revert to my base system image which is simply an image of my hard drive about a day after I installed Windows 7. It's configured the way I want it and has all my basic software/drivers installed. For me, it's the equivalent of formatting my hard drive. Even though most people use this method or something similar to simply backup their boot disc, you can use it to back up any disc you have.