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Ubuntu.
This is altogether unreproducible here. Using a separate partition for
/boot is a common configuration (the system I'm typing from is set up
this way), and update-grub has long supported it.
Is your /boot filesystem not mounted at /boot, or is it not listed in
/etc/fstab? update-grub calls boot_device=$(find_device "/boot") to
determine whether /boot is a separate filesystem, and find_device is a
function that looks up the mount in /etc/fstab. The only way I can see
this failing is if one of the above two conditions aren't satisfied.
** Changed in: grub (Ubuntu)
Status: New => Incomplete
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Incorrect paths in menu.lst with separate boot partition
https://bugs.launchpad.net/bugs/317085
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