How to repair a Windows7 boot sector on a secondary hard disk?

I've used Ubuntu to repair many MBR issues with Windows drives.

Boot from a USB with Ubuntu installed: http://www.ubuntu.com/download/desktop/create-a-usb-stick-on-windows

Install Boot-Repair: https://help.ubuntu.com/community/Boot-Repair

On the Main Options screen of the Boot-Repair GUI is the checkbox "Restore MBR".

Another link if you want more detailed steps: http://www.howopensource.com/2011/08/restore-mbr-from-ubuntu-live-cd-usb/

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In response about GRUB, here are commands to repair without using Boot-Repair.

On terminal:

Install ms-sys: sudo apt-get install ms-sys

List drives: sudo fdisk -l

Run MBR command and replace [drive]: ms-sys --mbr /dev/[drive]

For example: ms-sys --mbr /dev/hda

Boot from a Windows 7 Install/Repair disk. Even if it can't detect your Windows installation, you should still be able to get to command prompt to fix the MBR.

Once you're there, use DiskPart to activate the volume you want to repair. Type the following (line return = enter. Be sure to replace the "X"):

diskpart
List vol
select vol X

(Where X is the volume you wish to repair).

active
exit
cd /d X:

(Where X is the volume you wish to repair.

Now type bootrec /fixmbr which should fix the MBR. Depending on what's actually causing the problem, you may also need to use the fixboot and rebuildbcd arguments with bootrec.

If you can't find/use a Windows 7 Install/Repair disk, try Hiren's BootCD, it contains BootRec.exe within it's DiskMan 4.2 tool.