I explained slightly wrong, since my memory was vague. The old mdadm
2.7.1 in ubuntu probably makes the map file ok, but it won't get carried
across onto the rootfs. mdadm 3.1.2 wanted to place the map file in a
different location and failed. my solution at the time was to change the
location, and then copy it over to the rootfs once it is mounted. an
easier solution (and the default with upstream mdadm 3.1.4) is to use
/dev/.mdadm for the map file. as the devices is carried over to the
rootfs from the initramfs, this works better.

-- 
initramfs missing /var/run/mdadm/ dir (loosing state, race, misconfig)
https://bugs.launchpad.net/bugs/550131
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