More news:

I rebooted my system and looked in the grub menu (hit ESC) at the prompt. It 
listed 2 kernels for ubuntu 9.04.
2.6.28
2.6.27

I choose the second one and got dropped into the same recovery shell.
But this time, mdadm was able to build my array WITHOUT loopback
workarounds! It does however still use /dev/md/* rather than /dev/md*

I'd put my money on 2.6.28 being broken somehow?

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no block devices found after an upgrade from 8.10 to 9.04 on a soft RAID1 system
https://bugs.launchpad.net/bugs/358054
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