No one is faulty here.
* Grub2 is installed on the MBR to be the default bootloader of your system.
* Windows ME implements a protection scheme that check wether the MBR has been 
modified or not.
For some reason, Windows failed to detect Grub Legacy (well, there I can think 
that Windows ME was faulty here). But afaik, there was no workaround in Grub 
code to support Windows ME. Also, the MBR code hasn't really changed between 
Grub Legacy and Grub2, so I see ne reason why Windows ME complain. Have you 
checked if there's a way to deactivate this behaviour under Windows ME?
Also, if you are fluent with command lines, can you please send the output of 
the command (suppossing /dev/sda is your boot device)
~$ sudo dd if=/dev/sda bs=512 count=1 | hexdump -C
in these two different cases
* With Grub2 installed and Windows ME complaining about a virus in the MBR
* With ntldr installed (e.g. after a fixmbr)
This will dump the content of the MBR into hexadecimal.

-- 
when i boot in to win me It thinks I have a virus in mbr 
https://bugs.launchpad.net/bugs/410548
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