My work around for this which I have been doing for some time is to just
edit my Grub boot line, boot into Ubuntu then alter my menu.lst back to
how it should be. The culprit for me is always the following line for
each kernel listed:

root            (hd0,1)

For whatever reason after a kernel update all entries are changed to
"root (hd1,1)", changing back to the above fixes the problem each time.

Perhaps a better approach is needed to updating the menu.lst file before
more technical measures are attempted. If the script looked at what was
already set and just mimicked it for the new kernel instead of guessing
every time then this issue would go away.

-- 
grub guessed BIOS disk order incorrectly
https://bugs.launchpad.net/bugs/8497
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