Windows 7 Forums
Welcome to Windows 7 Forums. Our forum is dedicated to helping you find support and solutions for any problems regarding your Windows 7 PC be it Dell, HP, Acer, Asus or a custom build. We also provide an extensive Windows 7 tutorial section that covers a wide range of tips and tricks.

Windows 7: BOOTMGR is on the wrong drive? Partition marked as SYSTEM

11 Aug 2010   #1

Windows 7 Home Premium
BOOTMGR is on the wrong drive? Partition marked as SYSTEM

Hello all,
Just got a new motherboard yesterday so I hooked it all up, connected the SATA hard drives in the same position ports on the new motherboard as they were on the old one. Re-installed WIndows 7, and it's working fine. Installed onto C:\ which is correct, however I noticed that the 'boot' folder and the 'bootmgr' file is on another hard drive, Z:\. This is my 1TB hard drive which I now want to put into an external enclosure, but when I disconnect it from the motherboard, Windows doesn't boot up. It says 'bootmgr is missing', so I tried to do the repair startup thing using the Windows 7 Install DVD and still it doesn't work.
I noticed on disk management that the 1TB hard drive is marked as 'active, system and primary partition'. I managed to get rid off 'active' but now it is still marked as 'system, primary partition'. Is there any way that I can move the boot stuff onto my normal C:\, and change the 1TB hard drive to just 'primary partition'?

This is the report from BCDEDIT.

Microsoft Windows [Version 6.1.7600]
Copyright (c) 2009 Microsoft Corporation. All rights reserved.
Windows Boot Manager
identifier {bootmgr}
device partition=Z:
description Windows Boot Manager
locale en-US
inherit {globalsettings}
default {current}
resumeobject {13c7c901-a5c4-11df-a661-b3dd4177ad56}
displayorder {current}
toolsdisplayorder {memdiag}
timeout 30
Windows Boot Loader
identifier {current}
device partition=C:
path \Windows\system32\winload.exe
description Windows 7
locale en-US
inherit {bootloadersettings}
recoverysequence {13c7c903-a5c4-11df-a661-b3dd4177ad56}
recoveryenabled Yes
osdevice partition=C:
systemroot \Windows
resumeobject {13c7c901-a5c4-11df-a661-b3dd4177ad56}
nx OptIn

Someone please help!
Thank you. :)

My System SpecsSystem Spec
11 Aug 2010   #2
Microsoft MVP


This is why only the target HD should be plugged in during install.

Boot the Win7 DVD Repair console, click through to Recovery Tools list to open a Command Line to mark the Win7 partition Active using Diskpart: Partition - Mark as Active

Close Command box, return to Recovery Tools list to run Startup Repair up to 3 separate times with reboots to write the MBR to WIn7.
My System SpecsSystem Spec
11 Aug 2010   #3

Windows 7 Home Premium

Thanks for your reply.
The C:\ is already marked as 'boot, page file, active, crash dump, primary partition'.
Would it make a difference if I was to do what you suggested?
My System SpecsSystem Spec

11 Aug 2010   #4
Microsoft MVP


If C is already marked Active, then you are good to go with Startup Repair run from booted DVD/CD up to 3 separate times with reboots, no matter what messages are given.

You need to write System MBR to C which Startup Repair is automated to do if run enough times.

Make sure 1 tb is unplugged.
My System SpecsSystem Spec
26 Sep 2010   #5

Windows 7/ Ubuntu

Thought it would be better to bump this topic than start a new one:

This is the first time I've heard that Startup repair needs to be run more than once. Can you tell me why so I know when to try this and when not to bother?

Startup Repair - Run 3 Separate Times Here is a link to a tutorial about it, but it doesn't actually answer why.
My System SpecsSystem Spec
26 Sep 2010   #6

Windows 7/ Ubuntu

Another question: Should I rename/move the stupid boot files that Windows put on the storage drive before I disconnect it so I don't have problems when I reconnect it? I assume I would do this at the repair console command prompt of course.

(So ANNOYING that Windows would ever put the boot files there. Grrrrrrr! And why, since the DVD gives such nice instructions, doesn't it say to run the Startup Repair 3x??? It took me 4 days to find this. That's my bitch for the day.)
My System SpecsSystem Spec
27 Sep 2010   #7
Microsoft MVP


Win 7 Startup Repair automates all of the bootrec and boosect boot repair commands as well as myriad tests and fixes. It must run them in a certain order and requires reboots to know if repair is sufficient. By the second Repair it decides if it must repair or rewrite the MBR but that sometimes requires more than one pass.

Win7 will put boot critical (System) files on first available partition marked Active, which is the reason to unplug all other HD's during install, make sure no data drives are marked active, and if possible plug target OS drive into DISK0.

In your case, I would mark Win7 Active using DISKPART from booted DVD Repair console or Repair CD, mark Data drive Inactive, power down to unplug Data drive, swap its cable to Win7 or make sure Win7 HD is set first to boot in BIOS setup, then boot DVD/CD to run Startup Repairs. Partition - Mark as Active - Windows 7 Forums.URL

When you plug back in data drive, you can remove the hidden boot files, move data off to clean and format HD or partition, format using Disk mgmt.

If you will post back a Disk Management screenshot we can make sure there are no suprises.
My System SpecsSystem Spec
27 Sep 2010   #8

Windows 7/ Ubuntu

OK no one answered me but here is my solution:
Running Startup Repair 3x did not work. Neither did FixMbr and Fixboot.

Simple instructions for geeks:
*Plug in ONLY the Windows drive
*Double check that it's the Windows drive...Seriously. This was my mistake.
*Type Bootrec /RebuildBcd at the Repair Console command prompt. (See below for safer backp method)
*Reconnect the additional drives
*Delete or move the boot files on the additional drives via the Repair console. (They are C:\bootmgr, and C:\boot\bcd.) ***Type Dir first to make sure you're not in the Windows partition.
*Reboot into the BIOS and make sure the hard drives are booting in the right order.

Comprehensive Safe(r) Instructions:

*Note: this solution is not for Dual booting systems -- just single boot into Win7 or Vista.

First make sure the correct hard drive is plugged in. Embarrassingly, this was how I got into this mess. (I.T. geeks always ask themselves "is it plugged in," every step of the way.) After unplugging the other drives, verify you have the right Windows drive in your BIOS -- hold down the Del or F2 key (check your boot screen if not.) If you can't tell by reading the drive's name, see if you can find where it tells you the size. Still can't tell? Move on to the next step.

--To unplug a hard drive, shutdown, unplug the computer from the wall -- the whole power strip. Press the power button for 20 or 30 seconds to discharge. Then open up your computer and, on the back of the hard drive, just unplug the single-colored cable only. Don't bother with the multicolored one with bundled wires. That's for power, and would be fine too but it's usually tighter and more difficult.

With only the Windows drive plugged in boot into the Repair disk and go to the Command Prompt. Verify you're in the write disk and partition by typing C: then type DIR. Is Windows listed? Does it look like your C: drive? No? Go to another partition by typing D: or E: or F: ...etc., then DIR until you find Windows. (See **Note below if your drive letters are changed.) No Windows? Wrong drive! Shutdown and connect another. Mine was on C:
cd boot
attrib bcd -s -h -r
ren c:\boot\bcd bcd.old
Bcdedit /export C:\Bcd_backup
Bootrec /RebuildBcd
Voila! Windows should now boot without the repair disk in the drive. It is worth noting that you may have to mark your partition as active first then run my commands again. As stated above: "Boot the Win7 DVD Repair console, click through to Recovery Tools list to open a Command Line to mark the Win7 partition Active using Diskpart:"

Now you need to delete the boot files on the other hard drives or things will be a mess again. Shutdown and reconnect 1 drive at a time to avoid confusion. Disconnect the Windows drive just in case.

Reboot without the repair disk to test if there are boot files on the drive. If you get a "operating system not found" message there are none and you're virtually done! Skip down to ~Almost Done!~ If you get a bcd message again like, bcd/ "winload.exe is missing or corrupt," there are boot files to delete.

Reboot into the repair command prompt again. Find the partition with the offending boot files on it by typing it's letter followed by colon, such as C: then type "cd boot" without quotes. The command prompt will change to C:\Boot>. If it says it cannot find the path, then there is no boot info on that partition. Try another letter. If no partition other than X (your repair disc) has a boot folder you're all good. Move on to the next hard drive.

**Note: the drive letters in the Repair console will be different. This is why I encourage disconnecting the Windows drive to avoid confusion and mistakes. Your C: drive may look like your G: drive, and your M: drive may be missing. Don't freak out! It's only temporary. The partition letters will be in order starting from C:, so C:, D:, E:, F:, and X: will be be your repair disk drive. It will ignore your custom drive letter changes like M: and V:.

Assuming you've found the boot folder on drive C:\boot
attrib -s -h -r C:\boot\*.*
ren bcd bcd.disabled
attrib -s -h -r boot*.*
ren bootmgr bootmgr.disabled
attrib -s -h -r bcd*.*
move boot*.* C:\boot
move bcd*.* C:\boot
ren C:\boot C:\Dont_Boot

(For the simple but messy method skip the optional steps.)
attrib -s -h -r boot*.*
attrib -s -h -r bcd*.*
attrib -s -h -r C:\boot\*.*
move boot*.* C:\boot
move bcd*.* C:\boot
rmdir C:\boot /s
All gone now. This simply backed up the files by renaming them and then moved them to the Dont_Boot folder. For neat freaks: Once you boot into Windows with the extra drive connected you can delete the Dont_Boot folder. If Windows gives you a hard time just Google a program called Unlocker and use the instructions --- or just leave it. :) -- or use the dangerous method.

~Almost Done!~ Now shutdown and disconnect this drive. Reconnect the Windows drive again ONLY, in order to get it to say Drive0. Restart into the BIOS and make sure it's Drive0. Press F10 and Y and shutdown.

Connect all of your drives. Restart into the BIOS and ensure that Windows is still Drive0, Then go into the boot options and make sure that the Windows drive is the first Hard drive to boot. You can leave the CD as the first boot device as long as the Windows drive is the first actual hard drive.

Remove the repair disk from the DVD or USB port and restart.

My System SpecsSystem Spec
27 Sep 2010   #9
Microsoft MVP


I did in fact answer you and gave you the steps which have worked successfully here hundreds of times for your exact problem. Sorry I didnt' reply sooner but I was surfing in Mexico.

Startup Repair run 3 separate times should work if you marked the Win7 partition Active first.

Then if you also marked the data partition Inactive, the boot files should be able to be deleted if Windows in you unhide them in Control panel>Folder options>View, since the data drive will no longer be System Partition.

Of course there are certain cases where repair functions won't work as they should (e.g. no installation appears to repair, System not removed from data drive when written to 7) and yours might be one of these. There are workarounds for most of these instances.

It appears you are an above-average experienced User, and have learned a lot more from this experience. However if we tried to give the lengthy procedure you posted, almost no one would even bother to try it due to it's complexity.
My System SpecsSystem Spec
22 Jun 2016   #10
Paul Anderegg

Windows 7 32 bit

I am having a problem even getting the repair console to run.......keeps saying wrong Windows version.

Heres my issue. Started with Win 7 Pro for an MCE HTPC. OS was getting unstable, can't do clean install without loosing DRM and all TV recordings. Put a new double the capacity SSD in, fresh install of Win 7 Pro, and dual booted into the old MCE until I was done watching all the copy protected shows, then upgraded the old SSD to Win 10 just for kicks.

So, now I want to use that old SSD Win 10 thing for some other project, but cannot for the life of me remove it from the system without killing Win 7 Pro MCE boot capability. I already removed Win 10 from boot options in msconfig, but when I physically remove that old SSD, I get bootmgr not found. Have tried running Win 7 install disk, but when I click repair, it says wrong version. Win 10 repair runs, but reboots and no fixes.

I have marked my new Win 7 partition ACTIVE, and created a new 105MB NTFS partition on that same disk, but that is as far as I am able to go without more assistance. I have an image of the Win 7 install saved, but that is pointless as a failsafe if that damn old SSD isn't left intact right?

How do I go about fixing this issue? I was tempted to copy past the hidden boot files on the main disks, or clone the hidden partitions, but don't wana hose 2TB of copy protected DMR shows

My System SpecsSystem Spec

 BOOTMGR is on the wrong drive? Partition marked as SYSTEM

Thread Tools

Similar help and support threads
Thread Forum
EFI system partition on wrong drive
How do I get the efi partition on the c:\ drive????
Installation & Setup
The wrong drive is marked as "system"
I recently installed Windows 7. I have four partitions . Windows is installed on C:, and I also have D: , E: and G: as storage partitions . However, although C: is the boot partition it managed to mark G: as the system partition. This is causing a few problems with the Windows 7 backup feature...
General Discussion
Marked wrong partition as active, don't have access to Windows 7 DVD
Okay first of all, I don't know if this is the correct section. I marked the wrong partition as active in Windows 7, the problem is that I do not have access to a Windows 7 DVD to use diskpart. And I don't have access to any other computer at the moment. The only thing I have access to is an old...
General Discussion
System Reserved partition on wrong drive.
Hello, I recently bought a SSD to install my OS on it and use my HDD for other files. But when I tried to install the OS with only the SSD, it gave me an error: “No bootable partition” Then I tried with my HDD and SSD together and then it gave me the error: “Cannot boot from cd: code 5” So...
Installation & Setup
Marked wrong drive as active need help
So I did something really stupid and believe when I was looking around that I marked both drives as active and it moved my secondary drive to the front in the space as disk 0 and moved the windows drive to disk 1 and thanks it is supposed to boot from the wrong drive. I have no windows 7 recovery...
Hardware & Devices

Our Sites

Site Links

About Us

Find Us

Windows 7 Forums is an independent web site and has not been authorized, sponsored, or otherwise approved by Microsoft Corporation. "Windows 7" and related materials are trademarks of Microsoft Corp.

© Designer Media Ltd

All times are GMT -5. The time now is 05:59.
Twitter Facebook Google+