Windows does not like to be a slave.
Try these commands at that 'grub>' prompt (this is NOT an MS-DOS prompt, this is the grub command line):
map (hd0) (hd1)
map (hd1) (hd0)
These commands do the following:
1 - set the 'root' (in grub-speak, not linux-speak) location to the master boot record on the SECOND disk (first would be hd0).
2 - tell windows that the first disk is the second
3 - tell windows that the second disk (that's the windows disk) is first, this is where it wants to be
4 - tell grub to load another bootloader at the master boot record on the second disk (that's the windows MBR)
5 - tell grub to boot windows
If this works, then these are the commands that need to be listed in the /boot/grub/menu.lst file, in your Windows entry. You can edit the file with a text editor, like nano or vim, from linux. Then come back to the forum and tell us it worked, so others may benefit. If this doesn't work, post your /boot/grub/menu.lst here.
Any words you don't understand, try googling 'wiki <word>'
Welcome to linux.