Is this for grub - the "Advanced" option in the last box when you select options for install?
You can have grub where you please but if you don't put it in the MBR of the first disk you must have something to "lead you right" - a change in the boot loader already there or a change in the boot order in BIOS
If not the computer (obviously) just boots what ever is on the first disk.
You could try to repair grub and put it in (hd0)
http://www.linuxmint.com/wiki/index.php ... _your_grub
In the menu.lst there is an example how you add an existing Windows to the boot options
You may have to use the live CD for this