/etc/grub.d/30_os-prober uses os-prober to determine the parameters to
pass to linux. os-prober in turn looks at what is passed to the kernel
in that system's /boot/grub/grub.cfg. Since that system is a copy of the
main one, its grub.cfg has the main system's UUID for the root=
parameter.

That is my guess of what is happening at least. If I'm correct then
booting/chrooting into the backup system and running update-grub ( or
manually fixing the root= in the backup's grub.cfg ), then booting into
the main system and running update-grub there should give you a working
entry for the backup system.

-- 
update-grub sets wrong root argument
https://bugs.launchpad.net/bugs/508901
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