generally speaking, linux systems see partitions as partitions not standard
drives like windows. windows sees c: d: e: etc. while linux will see sda1,
sda2, sda3. or hda1, hda2, hda3. I say generally speaking because i'm still
fiddling and can only speak for debian based distros.
As for the updater trying to change your boot parameters I have no idea. That
sounds a bit funny to me. Do you have grub bootloader handling your boot
options? or are you using windows bootloader?
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