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Linux works fine, but when I try to boot windows with GRUB, the screen just goes black (The computers still on), and I have to restart and use linux. I use linux more often than windows, but I still have to do some things on it.
fdisk -l is a command that has to run with root permissions.
The location of menu.lst may depend on your distribution. Have a look in /boot/grub.
For grub.conf look in the same directory or /etc.
Most probably the partition number has changed. Once you locate menu.lst, you'll find that the partitions are addressed something like (hdx,y). x addresses the drive. hd0 is the first drive on the controller. y points to the partition. If you previously had 3 partitions (Linux, something, Windows), Windows would be on hd0,2. After deleting partition "something", Windows would change to hd0,1. Change this parameter below "title windows" accordingly. You need root permissions to be able to save the changes.
My Pc came with a small hidden partition before the main Windows XP parition. This is apparently used for restoring Windows. Some Linux distributions would try and set this first partition sda1/hd0,0 as the Windows partition and the boot into Windows failed because what I needed was sda2/hd0,1. When I first installed Linux I made the mistake of thinking that my Windows installation had been trashed. I wonder whether this 'empty first partition' was important to your Windows boot.