@Trenton D. Adams,

Just to make sure, did you add the raid through the following commands:
1) mdadm --create /dev/md0 --level=<level> --raid-devices=2 /dev/sda3 /dev/sdb3
2) mdadm --create /dev/md1 --level=<level>  --raid-devices=2 /dev/sda5 /dev/sdb5
?
If you do this, then you should not have to do anything more that this. Is you 
/etc/mdadm/mdadm.conf not getting updated inspite of this? Or else, what 
command did you use to get your raid under md?

-- 
post installation handling of raid devices on boot
https://bugs.launchpad.net/bugs/617725
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