I just ran into the Ubuntu 9.04 Jaunty mdadm problem last night. I did an online upgrade from 8.10, on which I had a raid1 array for the /home filesystem. The boot would stop in the middle and drop the console into a shell, complaining about mounts with /dev/md1 and other raid filesystems. There were no raid devices at all, /dev/md1, /dev/md2 etc. There were odd files named /dev/md_d1 (as I recall from memory). I noticed that there was a new file /etc/mdadm/mdadm.conf as well as the /etc/mdadm.conf which i was familiar with. I concatenated my old /etc/mdadm.conf with the new /etc/mdadm/mdadm.conf (which comments but no entries).
cat /etc/mdadm.conf >> /etc/mdadm/mdadm.conf
Then I ^D-ed out of the maintenance shell, and the boot continued successfully.
It's very odd that they moved the location of mdadm.conf from /etc to /etc/mdadm and did not migrate the entries.
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