I've recently run into this problem. From my own experience, and looking
around on the net, the cause seems to be that something in the handling
of chainloading or drive mapping has changed since grub-legacy,  and
Windows 95/98/ME thinks that it was booted from the MBR of a drive with
grub on it instead of its own MBR (thus the false-positive bootsector
virus detection and the use of compatibility mode). If the machine was
booted with grub-legacy, or if BIOS is set to bypass grub2 and boot
directly from the Windows' drive,  Windows detects its own MBR and boots
normally.

Grub2 isn't doing anything with the MBR(s) that grub-legacy didn't do.
What it *is* doing, however, is setting the machine up in such a way
that Windows checks the wrong disk when doing the MBR check, sees the
Grub MBR, and thinks the MBR has been modified.

In short, there seems to be a regression between "map" in grub-legacy
and "drivemap" in grub2 (or perhaps between "chainload" in grub-legacy
and grub2) that causes Win95/98/ME to check the MBR on the wrong drive
when booted from Grub2, but not when booted from grub-legacy or straight
from BIOS.

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https://bugs.launchpad.net/bugs/410548

Title:
  when i boot in to win me It thinks I have a virus in mbr

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