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Here's my setup. After I installed a new SSD, I have:

Grub is MBR on sda and set to boot from BIOS. I prefer to not change this; grub is much preferable as a boot manager.

I've run update-grub from Ubuntu and grub seems to be correctly configured as all options are available: I can boot any of the 3 Windows partitions and Ubuntu. I also ran the repair tool to get Windows to add both installations to BCD.

At present, choosing particular options seem to have no effect; the old version of Windows on sdc1 always boots. I don't understand what is causing this, but I can't figure out what. How does grub and BCD play along? I can't find any docs on this.

My thought was to only boot Windows off sdb1, and then let BCD do the rest (present a menu to boot between sdb2 and sdc1, but I can't seem to get BCD to boot sdb2), but this has been unsuccessful.

My configuration files:

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Paste your grub.cfg file if using Grub2 or grub.conf file for Grub –  wbeard52 Jun 20 '12 at 3:10
    
@wbeard52: Added, thanks for looking. –  wuputah Jun 20 '12 at 6:22

2 Answers 2

up vote 0 down vote accepted

Here's how to fix this issue:

  • Unconnect all your other hard drives
  • Try to boot your computer, get a cryptic error
  • Insert Windows disk, run repair

I haven't tried reconnecting my other disks yet, but I am sure Windows is using the SSD now!

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On MBR dual-booting Windows 7 and Linux is pretty clear:

Always the MBR from first disk in boot sequence (set in BIOS) is loaded and executed.

This MBR can be from Linux then GRUB takes control or MBR is from Windows 7 then boot manager (bootmgr) takes control.

Boot Configuration Data (BCD) in Windows has eventually several boot entries and if so bootmgr displays them for selection by user. You can have boot entries for Windows 7 and for Linux in Windows BCD.

GRUB configuration data is stored in grub.cfg - here we can have several boot entries for Linux and Windows. grub-install utility automatically scans and adds entries for all installed operating systems (Linux and Windows) no need to edit configuration manually.

For editing Windows BCD you can use bcdedit system utility or a graphical tool like Visual BCD Editor. Visual BCD Editor is capable of automatically adding boot entries for Windows installations. Next version of tool will add also Linux boot entries automatically.

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