I had a similar problem when attempting to move my root filesystem onto
a RAID-1 configuration.

mdadm wouldn't assmble the array while the initramfs was mounted, but
would when the normal root filesystem was mounted.

My mdadm.conf looks to be similar to those described, with a "DEVICE
partitions" line.

However, after a bit research, I think that my problem was with the
"HOMEHOST <system>" line.

mdadm uses HOMEHOST to determine which partitions to automatically
assemble into arrays.  When HOMEHOST is set to '<system>' mdadm uses the
hostname of the system.

Unfortunately, the initramfs file system doesn't set a hostname (i.e. the 
hostname of the system in initramfs is '(none)'), which doesn't match the 
homehost of the partitions in the array, which causes mdadm to not 
automatically assemble any arrays.
(The first 64 bits of the SHA1 hash of homehost appears to be the last 64 bits 
of the array's UUID.)

Explicitly naming the arrays using ARRAY lines in mdadm.conf causes
mdadm to assemble those arrays without using homehost  Alternatively, I
set HOMEHOST in mdadm.conf to match the hostname of the system.

I don't know enough about things to say what a general solution is, but
hopefully this explains the inconsistent behavior between the initramfs
image and the normal root filesystem.

-- 
[gutsy] mdadm, initramfs missing ARRAY lines
https://bugs.launchpad.net/bugs/136252
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