Comment 8 for bug 391044

i think my problem was installing as chainload then using the upgrade from legacy command (if i saw the option to install to the various mbr's on install i would have unset them to avoid overwriting the old grub)
then seeing grub2 on boot everything looks ok but upgrade-grub shows it isnt.
but dpkg-reconfigure grub-pc and going through the debconf options to install to the various mbr's makes everything ok again. just a note for anyone else who finds themselves here.
on a side note, the option to install to mbr's is now missing on freshly installing grub-pc, only the chainloading option is there, i take it this is the default now and not a bug