The solution to a damaged partition boot sector is to overwrite it with a new, properly configured one using the bootrec command.
Important: The following instructions apply to Windows 8, Windows 7, and Windows Vista. Boot sector issues also occur in Windows XP but the solution involves a different process. See How To Write a New Partition Boot Sector To a Windows XP System Partition for help.
Start System Recovery Options.
You have a few different options in regards to getting to System Recovery Options, all of which are detailed in the How To Access the System Recovery Options Menu section in the link above.
Open Command Prompt from the System Recovery Options menu.
Note: The Command Prompt available from the System Recovery Options menu is similar to the one available from within Windows and works very similarly between operating systems.
At the prompt, type the bootrec command as shown below and then press Enter:
The bootrec command will write a new partition boot sector to the current system partition. Any configuration or corruption issues with the partition boot sector that might have existed are now corrected.
You should see the following message at the command line:
The operation completed successfully.
and then a blinking cursor at the prompt.
Restart your computer.
Assuming that a partition boot sector issue was the only problem, Windows should start normally now. If not, continue to troubleshoot whatever specific issue you're seeing that's preventing Windows from booting normally.
Important: Depending on how you started System Recovery Options, you may need to remove a disc or flash drive before restarting.