It seems that still didn't fix it permanently.

At a certain ppoint things got really messed up.
Normally I have sda1+sdb1=md0 sda2+sdb2=md1 and sda3+sdb3=md2 on said system.
At one point md2 got somehow created from sda and sdb, md0 and md1 were then 
created from md2p1 and md2p2 (!!).
And this thing booted... (md0 is /boot, md1 is /)

I re-upgraded from hardy to lucid in the mean time, which didn't fix
anything either.

As I'm consistently noticing the problem seems related to mdadm
detecting a superblock on the full disk device, instead of the
partitions, I added the specific partitions to mdadm.conf:

/etc/mdadm/mdadm.conf:
DEVICE /dev/sda1 /dev/sda2 /dev/sda3 /dev/sdb1 /dev/sdb2 /dev/sdb3

This seems to consistently solve the issue in my case now.

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https://bugs.launchpad.net/bugs/27037

Title:
  mdadm cannot assemble array as cannot open drive with O_EXCL

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