Nevermind Bret, I fixed it after trawling the intarweb for a few more
minutes.

I ran:
sudo dppg-reconfigure mdadm

Accepted all the defaults. If you've never played silly-buggers with
your kernels, this *might* fix it for you, but as it was, I have built a
couple of kernels before and the initramfs-update was trying to write to
one of those (that I don't use). So I had to remove all the custom
kernels and reinstall 2.6.22-14-generic in synaptic. I then ran dpkg-
reconfigure again, it wrote the to correct kernel image, I rebooted, and
my RAID works. Woo!

Oh one important (I think) note, my mdadm.conf contains the UUID of my
HDs, not names because the names seem to be quite fluid (they kept
changing name every boot). If you're not set up like this, I suggest
doing so.

-- 
Software RAID sometimes fails to assemble arrays on boot
https://bugs.launchpad.net/bugs/114170
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