@Xtigyro

I take a closer look at the previous steps, I think the one that
breaks is the very first grub-install, while the active flag is in
ext3 partition. After that, no matter what you do, the result would be
the same. Windows keeps a mapping of partition and drive letter in the
registry. When you use grub-install to install to mbr, it invalidates
the mbr checksum, and windows rebuilds the mapping. But as the ext3
partition is active, it became C:\, and the original windows become
D:\. this would cause problem as some system files can't be found. It
doesn't matter if you change the active flags back or rerun
grub-install, it's the same mbr, and windows won't refresh the mapping
again.

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