After updating to 9.04, I experienced a similar problem.
I have three md devices: md0 (/dev/sd{a,b}1, swap), md1 (/dev/sd{a,b}2, root),
and md4 (/dev/sd{a,b}3, home). On boot, mdadm would incorrectly detect that
/dev/sda was an md device and create it. Upon inspection (using mdadm -E),
/dev/sda, /dev/sdb, /dev/sda3, and /dev/sdb3 all had the same super block.
Zeroing the /dev/sda and /dev/sdb ones resulted in also zeroing the /dev/sda3
and /dev/sdb3 ones (which suggests that the /dev/sda3 superblock was being
detected as the /dev/sda one).
I changed my /etc/mdadm/mdadm.conf to have
DEVICE /dev/sd??*
rather than
DEVICE partitions
and the system booted fine.
While searching for this problem, I found that some people reported that
mdadm --incremental would not create their arrays properly whereas
mdadm -As worked fine. I extracted the initrd (kernel 2.6.28-11-generic)
and found that this is indeed how the arrays are being built. I didn't check
whether 8.10 uses --incremental or --assemble, but perhaps this is a starting
point for further investigation of this issue.
--
[gutsy] mdadm, initramfs missing ARRAY lines
https://bugs.launchpad.net/bugs/136252
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