I have the same issue.

The problem is that the /usr/share/initramfs-tools/scripts/mdadm-functions 
Is called before all drives has been initialized. 
I have 6 drives in RAID array. 2 of them are onboard SATA and 4 are on mpt2sas 
(SAS2008) card. 

Apparantly mdadm tries to initialize the array before all 6 drives have
been attached to the system

If i edit mdadm-functions to this everything works (ugly fix):

degraded_arrays()
   {
       sleep 15
   >---mdadm --misc --scan --detail --test >/dev/null 2>&1
   >---return $((! $?))
  }


This bug was introduced for when i upgraded from 10.04 LTS to 12.04.1
LTS Today!

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https://bugs.launchpad.net/bugs/990913

Title:
  RAID goes into degrade mode on every boot 12.04 LTS server

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