You might have mistakenly deleted essential boot files in the windows folder. Since Ubuntu gives you the ability to access and read and write files in the C:\ folder, its possible that you might alter Windows system files, which are generally unalterable when using microsoft widows.
This problem might also arise due to the use of Partitioning Applications, like gparted, to partition the main windows drive from ubuntu
Its possible is that you resized the ubuntu partition either using a partitioning app of some sort, or during installation, and the resize ate in into the windows system. This is a fatal error, and is seriously hard to resolve.
If you have a windows installation disc, put it into your disc drive and restart your machine and try to boot to windows, and then try the "System Restore" option