If your Windows partition will not boot, but you can still boot into Ubuntu using your dual boot option, then there is away to repair your Windows partition from within Ubuntu.
Check with Synaptic Package Manager to see if you have “ntfs-3g” installed. If you have not, install with Synaptic or type the following lines in the terminal:
sudo apt-get install ntfsprogs sudo apt-get install ntfs-3g
After that, right click on your Windows partition on your Ubuntu desktop and unmount it.
sudo fdisk -l
This will tell you what volumes exist on your system.
You will see an entry such as:
/dev/sda1 * 638 12312 93773824 7 HPFS/NTFS
Next, type: sudo ntfsfix /dev/sda1
This command will repair and re-mount your NTFS at sda1. If your windows volume is at “sda2”, then put “sda2” instead. It does not matter if you make a mistake here, use of this command on a volume which does not need repair does no harm.
Ubuntu can also be used to repair the Master Boot Record, but I would advise against the use of this method.
See link below for detailed intructions with screenshots: