Same problem here.

Installed hardy server amd64 from scratch, /boot is on lvm. Initially
there were no problems. After the first kernel upgrade (probably the
first, not 100% sure) got the directory structure warning. Kept ignoring
the warnings, the system was working fine. Until this last hardy kernel
upgrade, that would be linux-image-2.6.24-19-server, usual warning but
the system did not reboot anymore. Don't have access to the server
console, the admin that eventually restarted the server selected
LinuxOLD.

The warning is trivial to replicate: just install hardy server, tried
with i386 under virtualbox, and manually partition and put the whole
root on lvm (including /boot). After the system is installed, run apt-
get upgrade, the newer kernel will be installed. You will see the
directory structure warning. This test system rebooted fine for me.

See attachment for exact warning.

** Attachment added: "/var/log/apt/term.log"
   http://launchpadlibrarian.net/17670661/term.log

-- 
lilo + lvm2 don't work following upgrade to breezy
https://bugs.launchpad.net/bugs/23835
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