Windows – New drive does not boot after cloning mbr/partitions

Most probably there are couple of problems. One is the fact that you're copying only one of the OS partitions while the dualboot is usually handled by the Unix loader.

The other issue could be the software itself, since it does not copy the windows boot partition (the *:) correctly.

My suggestion is that if you want to copy only the windows OS, just go ahead and clone the unnamed partition and the one containing windows. Then disconnect the HDD, run windows installation disk or USB and select the repair option. This will almost certainly fix the boot process.

If you want to keep the existing state, do a whole disk clone, and you could use software later to move and resize the partitions as you wish. Hiren bootcd contains what you need for this. And you can use Rufus to make bootable USB

A little background

To understand what is happening, you need to know a little background about how Windows boots up. Optimally, Windows Setup stores Windows boot loader on a partition labeled "System Reserved". This partition is small and remains hidden by default to prevent accidental tampering. But it is also marked as "active", so that the firmware looks for boot loader in it. (There can only be one active partition per disk.) In Microsoft definition, a partition containing the boot loader is called "System Partition".

Windows itself is installed on the first visible partition. Starting with Windows 7, this partition always usurps the drive letter of C in all clean installations. Microsoft defines this partition as "Boot Partition".

There is one important details though: Windows stores the reference to the boot partition in the form of the unique disk ID plus partition number.

Side notes: Observant readers might have by now noticed that according to the definition I gave above, a "System Partition" is one that by default DOES NOT contain the system root, and the "Boot Partition" one that by default DOES NOT contain the boot loader! Yes! Welcome to world of inverse Microsoft definitions. For details, see: "System partition and boot partition" on English Wikipedia.

What's happening in your computer?

It is quite clear that both partitions labeled "System Reserved" in your computer are set to "active". This means the firmware would find those, depending on from which disk it tries to boot first. And in this case, it is trying to boot from your new disk.

But... upon reading the boot data, Windows bootloader tries to start Windows from the second partition in a disk containing a certain unique disk ID. That disk ID would be your old hard disk's ID. Hence, it is currently booting off your old hard disk. If you had removed your old disk altogether, you'd have noticed that you lost your ability to boot into Windows altogether, because the boot loader is looking for a disk that no longer exists.

When you say you cloned the two disks, you actually cloned their contents. Their hardware IDs are still what they were; they cannot be changed. What you should have done was to reconcile the boot loader's database, so that it points to the new disk instead of the old.

That's the reason behind the "Boot" attribute being on the wrong partition. Presence of the "Page File" and "Crash Dump" attributes on the wrong partition is the consequence of the wrong partition having received the C drive letter.

Okay... What to do now?

There is an easy way, and there is a technically correct way.

The easy way is to remove the old hard disk temporarily and try to boot your computer. The boot will fail, but the boot loader may be able to try and locate the Windows recovery environment, from which you can start a fully automated startup repair. If it didn't find it, you can still insert a Windows Setup USB, boot your computer from it, select "Repair this computer" and do the automated startup recovery. This easy way is time-taking but very foolproof.

The technically correct way is to edit the boot information database, known as BCD, and direct it to boot from the second partition of the new hard disk. Editing it is possible using a command line tool called bcdedit, but most people find it too complex. However, I myself prefer a third-party tool called Bootice.

In its BCD tab, you can clearly see an "Easy mode" button.

...and in the easy BCD editor, you can clearly see that it is possible to change the disk and the partition from which Windows boots.

This method is not foolproof, however. Be cautious. And make sure you have a backup first. Test your success by completely removing the old hard disk.