Narrowed this down to Cloud-init. Cloud-init is not selecting the right device, 
and is reconfiguring Grub to use /dev/sda:
Jul  2 16:53:10 ip-10-169-38-57 [CLOUDINIT] __init__.py[DEBUG]: handling 
grub-dpkg with freq=None and args=[]
Jul  2 16:53:10 ip-10-169-38-57 [CLOUDINIT] cc_grub_dpkg.py[DEBUG]: setting 
grub debconf-set-selections with '/dev/sda','false'
Jul  2 16:53:10 ip-10-169-38-57 [CLOUDINIT] __init__.py[DEBUG]: handling 
apt-pipelining with freq=None and args=[]

And the mounts:
$ mount
/dev/xvda1 on / type ext4 (rw)
proc on /proc type proc (rw,noexec,nosuid,nodev)
sysfs on /sys type sysfs (rw,noexec,nosuid,nodev)
none on /sys/fs/fuse/connections type fusectl (rw)
none on /sys/kernel/debug type debugfs (rw)
none on /sys/kernel/security type securityfs (rw)
udev on /dev type devtmpfs (rw,mode=0755)
devpts on /dev/pts type devpts (rw,noexec,nosuid,gid=5,mode=0620)
tmpfs on /run type tmpfs (rw,noexec,nosuid,size=10%,mode=0755)
none on /run/lock type tmpfs (rw,noexec,nosuid,nodev,size=5242880)
none on /run/shm type tmpfs (rw,nosuid,nodev)
/dev/xvdb on /mnt type ext3 (rw,_netdev)


** Changed in: ubuntu
       Status: New => Confirmed

** Changed in: ubuntu
   Importance: Undecided => High

** Package changed: ubuntu => cloud-init (Ubuntu)

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https://bugs.launchpad.net/bugs/1336855

Title:
  non-interactive grub updates for 12.04 break on AWS

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