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Upgrade-grub and boot-repair fails. Unable to boot one of my linux systems, is there a way around?

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http://askubuntu.com – I have three Linux and two windows systems on one computer. After updating the kernel on one (archlinux) and running update-grub on the default (BIOS) boot disk (Xubuntu 12.04), the boot menu does not report the archlinux system. After running boot-repair, I cannot boot the archlinux system by selecting it as the boot disk in BIOS because it now uses the boot configuration on the Xubuntu system instead of booting directly from its disk. I really need to be able to boot the archlinux system, how can I do this? Note: Bugs filed and notices made on this. (HowTos)