I think it was in 9.04 when udev switched to use mdadm --incremental.
So you reported what's discussed at
http://ubuntuforums.org/showthread.php?p=8407182, and experience those
Bug #550131 initramfs missing /var/run/mdadm dir (loosing state)
Bug #136252 [-UUIDudev] mdadm.conf w/o ARRAY lines but
I should elaborate - all arrays created BEFORE md66 still autoassemble
perfectly.
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mdadm does not remember its actions correctly
https://bugs.launchpad.net/bugs/469574
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