Okay guys, I am having a tough time tryin to figure out this one and I hope some of you can lead me to a right direction ..
My friend who has windows 7 as operating system, usually on boot up he has 3 options to choose inbetween and a 30 seconds to do so or it loads the default one. The default one was "Upgrade windows" or something like that, and he really got tired of seeing that massage and being on the pc as it starts to select the correct one so he went to windows 7 bootloader and chose to skip the 30 seconds time of choosing thinking it will auto start the correct one ... but instead now it doesn't have the seconds to choose and starts on the Upgrade option automatically, and that option is broken so nothing happens, if you restart the same thing over again ..

Now I had a similiar problem with my Kali linux but I managed to change the grub loader settings from a live usb ubuntu and I am wondering is that possible to do for this case on Windows? To access the boot manager, I think it is boot.ini file? Or anything else I could do to fix this?

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You can use EasyBCD to edit the Windows bootloader menu (including adding Linux boots to it too!). It's advertized (but free) as a way to setup dual-boots, and it's great for that, but you can also just use it to edit the Windows bootloader menu entries. That's what I've always used for that kind of thing, it works well (but watch out for factory-installed crapware (from the computer manufacturer, not Microsoft) that sometimes overwrites / corrupts the Windows bootloader, that is another recurring source of frustration, just remove any factory-installed crapware).

Hey Mike, the problem now is that I can't boot in the os, its in a countless loop restart - upgrade option, cant do anything if restart again it will go to the upgrade option again, it's not that I want dual os boot(I got easybsd for windows 8.1 and Kali on my laptop,it was the only thing that could bypass widnows 8.1 security not to boot other os)

Basically, what I should do is access somehow the boot manager that already is there and probably make it so it has 10 seconds or so time before it boots to the default option where I can select the correct position of the os. Do you understand what I mean? I think from live usb I should be able to access the windows files right? but then what to change the boot loader?

Or even better, according to this i can delete the unwanted boot entries, including the 1 that is default currently using msconfig, however will I even be able to start that 1 through live usb of ubuntu? Like, I am really out of ideas how to make it boot into windows now ...or install EasyBCD from the live usb ?

Oh, I see the problem now... So, even if you boot up using a liveCD/USB of Ubuntu, you can't even boot into Windows by selecting it in the LiveCD's grub menu? I'm pretty sure that's supposed to work, no?

In any case, unless you have a Windows restore CD to repair your bootloader, you will have to see what can be done from Ubuntu (or some other Linux LiveCD/USB). There seems to be a very easy way to restore the Windows bootloader from Linux but I have never tried this procedure. If that fails, then you should look into temporarily installing Grub on the MBR, to be able to boot to Windows, and then, restore your bootloader from Windows (with EasyBCD or BCDEdit, or some other Windows restore utility).

You can try the following:

Option 1:

  • Turn computer on. Press "F10" repeatedly (once or twice per second).
  • If prompted to "Edit Windows boot options...", press the escape key.
  • If the Windows Boot Manager screen appears ("Choose an operating system to start..."), select the OS you want to boot.

Note: If "F10" doesn't work, reboot and try another "F" key.

Option 2: Use "EasyBCD" as others have stated.

Option 3:

How to Manually Repair Windows 7 Boot Loader Problems

Option 4:
If you don't have the install DVD (or your install DVD doesn't have the "Repair your computer" option), you can create a bootable USB drive using WinPE 5.1 (it is for Win 8.1, but you should be able to use it for Win 7).

To create the bootable USB drive using Win 8 computer:

Demo 2: Installing Windows PE on a USB Drive

To create the bootable USB drive using Win 7 computer:

Download and install Windows Assessment and Deployment Kit (Windows ADK) for Windows 8.1 Update

  • Double-click "adksetup.exe".
  • You either choose Option A: "Install the Windows Assessment and Deployment Kit for Windows 8.1 to this computer" or Option B: "Download the Windows Assessment and Deployment Kit for Windows 8.1 for installation on a separate computer". (I chose Option B: "Download the Windows Assessment...", so I could save it and not have to download it again should I want to install it on another computer. If choosing Option B, write down the "Download Path" from this screen.
  • Click "Next"
  • Join the Customer Experience Improvement Program (CEIP): Choose "Yes" or "No".
  • Click "Next"
  • Click "Accept"

For Option B, after the download is complete:

  • Go to the "Download Path" you wrote down earlier
  • Double-click "adksetup" to install.
  • Click "Next"
  • Join the Customer Experience Improvement Program (CEIP): Choose "Yes" or "No".
  • Click "Next"
  • Click "Accept"
  • Ensure the following two checkboxes are checked: "Deployment Tools" and "Windows Preinstallation Environment (Windows PE)". Uncheck "Microsoft SQL Server 2012 Express" and "Application Compatibility Toolkit (ACT)" (and any of the others you don't want to install).
  • Click "Install" (if not an administrator, you will be prompted to enter the password for an administrator account)
  • After the installation is complete, you will see a screen "Welcome to the Windows Assessment and Deployment Kit...". Click "Close"

Note: You will need a USB flash drive for the next part. It will be formatted (everything will be erased from the drive). It needs to be at least 256 MB (so a 1 GB, 2 GB, 4 GB, 8 GB, etc will work).

  • Plug the USB drive into the computer that you installed the Windows Assessment and Deployment Kit on.
  • Click "Start"
  • Select "Computer"
  • Write down the drive letter associated with the flash drive. (I will call it "<USB flash drive letter>")

Open the ADK:

  • Start
  • All Programs
  • Windows Kits
  • Windows ADK
  • Right-click "Deployment and Imaging Tools Environment" and select "Run as administrator"

You will see the following prompt ">"
type: "dir" (to see the directory contents)

For 32-bit OS:

Copy files to temporary location:

copype x86 "C:\WinPE_x86"

Note: "C:\WinPE_x86" can be any location. It is a temporary location that we will copy the files to that we are going to be using. If the directory path contains one or more spaces, the location must be in double-quotes. The prompt will change when the copy is complete (from ">" to "C:\WinPE_x86"--or whatever you chose for your location).

Write files to USB drive:

MakeWinPEMedia /UFD "C:\WinPE_x86" <USB flash drive letter>:

ex: MakeWinPEMedia /UFD "C:\WinPE_x86" F:

Note: The double quotes around "C:\WinPE_x86" are only required if the directory path contains one or more spaces.

For 64-bit OS:

Copy files to temporary location:

copype amd64 "C:\WinPE_amd64"

Note: "C:\WinPE_amd64" can be any location. It is a temporary location that we will copy the files to that we are going to be using. If the directory path contains one or more spaces, the location must be in double-quotes. The prompt will change when the copy is complete (from ">" to "C:\WinPE_amd64"--or whatever you chose for your location).

Write files to USB drive:

MakeWinPEMedia /UFD "C:\WinPE_amd64" <USB flash drive letter>:

ex: MakeWinPEMedia /UFD "C:\WinPE_amd64" F:

Note: The double quotes around "C:\WinPE_amd64" are only required if the directory path contains one or more spaces.

For 32-bit/64-bit:

Connect USB flash drive to computer you want to boot WinPE on.

Set BIOS/UEFI to boot from USB flash drive by entering the BIOS/UEFI settings and changing the boot order and/or USB settings

After WinPE loads, a command prompt window will open. To see settings, type "bcdedit" and press enter.

To change the timeout setting:
bcdedit /set {bootmgr} timeout 20

Reboot.

If that doesn't fix it, follow the steps in the link above: "How to Manually Repair Windows 7 Boot Loader Problems"

Resource:
WinPE: Create USB Bootable drive

commented: Nice complete explanation! +14

Note: In WinPE, when in the command prompt window, you can type "exit" to reboot.

Thanks guys for your help :\ unfortunately after over 20 hours, still no success and I think I am giving up .. He'll be getting a new os, tried so many things even use the HDD as external to mine and use easyBCD to go in, it won't load past windows welcome screen, tried playing with /Boot/BCD , tried reparing it with easyBCD and so many things nothing really worked. Gave up :x

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