Windows have a tool for this purpose, called BCDboot.
If the system partition has been corrupted, you can use BCDboot to replace the system partition files with new copies of these files from the Windows partition.
When you have booted to the Windows disc, then go to the command prompt (see here) and type the following to recreate the BCD on the C drive:
attrib -r -s -h c:\boot\bcd - unhide BCD so it can be deleted
del c:\boot\bcd - delete the current BCD
bcdboot C:\windows - create a new BCD on the C drive
- Put the Windows installation disc in the disc drive, and then start the computer.
- Press a key when the message indicating
Press any key to boot from CD or DVD.... appears.
- Select a language, a time, a currency, and a keyboard or another input method, and then click Next.
- Click Repair your computer.
- Click the operating system that you want to repair, and then click Next.
- In the System Recovery Options dialog box, click Command Prompt.
- Try the bootec commands and then run StartUp Repair twice from your Windows Disk. Enter these commands:
From here you should be able to boot into Windows again.
If does not work, you can try to solve this problem using Boot Repair (as already mentioned),