I assume you're referring to the stage1.5 component, which by default gets installed into the sectors following the MBR. It can also be installed into the boot area of your Linux boot partition for filesystems that support it, and Windows stuff had better not be touching that.
Heck, stage1.5 is optional, so if you want you can have GRUB read the stage2 file directly off the hard drive sector-by-sector in the same technique LILO uses. I believe this is how RedHat's installer usually installs GRUB to be immune to apps that trash the spare sectors. (Of course, then you might be susceptible to geometry changes, just like when using LILO.)
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