One probably-not-as-easy-as-it-sounds idea: 
Have grub installer compute suitable error correction codes of the embedding 
area and save them somewhere there (after the core image, say). When Windows 
next time trashes it, when reinstalling Grub the installer could use the codes 
to determine which part of the embedding area has been overwritten (if the 
codes themselves have been rewritten, the information isn't complete but enough 
to be helpful) and try another area instead. Even though it'd mean having to 
reinstall grub maybe a few times, it should stabilize eventually (unless the 
windows things use up all available space). And it could (with user's 
permission of course) report the areas used automatically to developers.

This should require hardly any changes to grub, just a few extra pointer
bytes in MBR - the installer, however, would need some rather heavy
coding to pull this off.

-- 
grub fails after running Windows
https://bugs.launchpad.net/bugs/441941
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