recently after installing Linux or resizing partition using Gparted I came up with a boot problem of my windows instance. Solution is to boot from installation dvd. Then you have to choose language and go for repair console. Once it is open you can try these set of commands:
bootsect /nt60 all /force
Maybe this will fix your problem. I am not sure what should be the proper order of last two commands, but maybe it is irrelevant.