I see this problem a lot.
There is another post like this right now.
And I learned this the hard way my self.
If you have a dual boot set up and you want to remove one of the operating systems you should always set you system to boot to only the OS that will be left before you remove the other one.
This can be done using EasyBCD a free program that lets you modify your boot setup.
Set you computer to boot to the final OS, reboot your computer, make sure it boots without asking you which one you want to boot into, and then remove the other operating system.
It saves a lot of headaches.
Mike