I am facing this problem in all Ubuntu releases. I have two SATA and one
IDE hard disks. I use Smart Boot Manager to boot the system for multiple
Operating Systems. Grub resides in Ubuntu partition. I found that Grub
and Ubuntu installer do not agree about the sequence in which the drives
are enumerated. There is a confusion in deciding whether SATA or IDE
drives are to be enumerated first. After every kernel upgrade menu.lst
file has to be manually edited to correct the problem. I have noticed
that Fedora, Suse and Mandrake releases do not have this conflict.

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Kernel updater doesn't update grub's menu,lst correctly
https://bugs.launchpad.net/bugs/103297
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