Windows installation woes with booting and multiple hard drives

Have you ever had a computer problem that quickly became a lengthy nightmare to solve?

It seems that installing Windows can very quickly become a terrible nightmare. Imagine you find yourself in a situation where you installed Windows, but it does not seem to boot due to issues with multiple physical drives.  I quickly realized that it is much harder to get it repaired and working than it is for Linux.

The first thing to remember is that whenever you have multiple disks and install Windows on a second disk, but format the first disk that you had Windows installed, then Windows will not boot. This problem can be avoided through one simple method. Before installing Windows, disconnect from your motherboard all of the extra SSDs and HDDs that you do not plan to install Windows on and then put your Windows boot SSD into. Sometimes though, it is not possible to do that (or practical and as a result, it becomes a pain to deal with).

The other is on your motherboard, I recommend that for all installations for Windows to connect to the SATA ports that are attached to the PCH and not a third party controller. Motherboards will often have their first few SATA ports connected to the chipset and then the rest provided by a third party. That third party controller often has problems with Windows and even when it works is often quite a bit slower.

To solve any boot problems that you have, the first thing you have to have handy is the boot DVD (or USB stick) that you used for installing Windows to begin with.

Try the bootrec first

Once you have the recovery in, set the BIOS to boot from the CD or USB. One important consideration – if you installed Windows as a UEFI boot, make sure that the DVD or USB is also set to UEFI. Otherwise, if you installed Windows as a “normal” boot, make sure that Windows is set to normal mode. This will not work otherwise.

Click on the Recover your Windows installation and the Advanced System Options

Open up a command prompt. Type in the following commands (note that they are not case sensitive):

bootrec.exe /FixMbr

bootrec.exe /Fixboot

Try rebooting Windows and seeing if the installation is detected. If not, then you may need to rebuild entirely.

bootrec.exe /RebuildBcd

This should rebuild the entire Boot Configuration Data (BCD). The command will also scan your disks for any active installations of Windows and possibly Linux as well (although from my experiences, that can be unreliable).  The menu will search and put a list of installations that you can then add to the menu.

Set the drive as the active partition

You may get an error like “Element not found”, that means that it does not know which drive to use. You must set up the drive that you want to use as the active partition.

To do this, when you have the drive that you need to boot from.

bootrec.exe /ScanOS

This will tell you what installations are available on which hard drives.

I would recommend using Diskpart to resolve the problem.

Still in the command line, type the following:


List Disk                    Provides a list of all of the disks.

Select Disk  “A”           “A” being the disk number that you want to install on.

List Partition              This will list the partitions in the disk.

Select Partition “B”         “B” being the number of partition again.

Active                        This will set the partition


Now try the step below to try to build a boot manager to that disk or  use the 3 bootrec commands again for booting from multiple systems.

Fixing the Boot Manager

You will end up with “bootmgr” is missing.

Type in the following:

bcdboot C:\Windows /l en-us

Change the “C” for whatever hard drive is appropriate and the “en-us” to whatever language you are working with. I recommend for Canadians who primarily use English to use En-US and not the Canadian multilingual standard as that can make the E have an accent unintentionally.

This will create an entirely new Bcdboot in the C drive.

Some other useful hints when installing Windows

  1. If you can, burn the Windows disk ISO as a DVD (you will need a spare DVD and a DVD burner). USB disks sometimes have problems that can be avoided entirely with the DVD.
  2. Also, it helps to keep a spare USB disk with a Linux distro that you are familiar with at all times.
  3. If you are planning to boot Linux and Windows, install the Windows installations first.
  4. Always keep a PS/2 keyboard or mouse on hand. Often when things go wrong with USB, PS/2 is the only interface left working.
  5. I recommend that you disable any Fast Boot functions from your motherboard, as they tend to cause problems.

After the clean install

  1. I recommend for power settings for recommended turning  the “put the computer to sleep” to never if you plan to leave the computer on all the time, especially when copying large files
  2. Install the drivers right away (unfortunately, most hardware will not be recognized without drivers in Windows).
  3. Install a firewall immediately (sadly the nature of WIndows makes it vulnerable), and get the start up updates right away
  4. Activate Windows sooner rather than later to get rid of the annoying messages (phone is the easiest way, if the online activation fails – which it often does for me).

You can use something like Ninite to install applications quickly if need be.

Conclusions and feedback for Microsoft

To begin with, hopefully this has been of value to you and I have saved you from many hours of needless extra work. I know that getting Windows to boot after system changes can be a pain.  For me, the whole reason why I did this clean install was because I was changing my system, due to a dead motherboard.  Upon replacing the new motherboard and installing the drivers, the USB would not play nice and I had to install a PS/2 keyboard to get anything done.

I feel like this is much harder than it needs to be.

  1. Microsoft needs to provide better tools for boot repair and system start-up.
  2. Better quality drivers need to be build into Microsoft products so that they actually work on launch.
  3. There should be a longer than 3 day grace period as well for Activating Windows

I’m going to be moving towards Linux as my main operating system for this reason. It is just must less painful to deal with on a day to day basis. I just wish that all of my applications supported Linux and that hardware support was better (particularly video card drivers).

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