Blimey, talk about knowing how to make a girl feel guilty! It was me who caused Mike to insert a slightly longer timeout into the boot for the second disk.

No problem, the fast boots are only a patch away. I can well see why that delay is necessary, if you have two different disks, or something.
I can't fathom (but then I haven't looked) why the device driver for the AT disks in the unit is unable to determine the presence of a disk drive and then respond to the kernel so that it can take appropriate action. This would be the case under Slowaris and FreeBSD; how come not with Linux? Or is this just too obvious?
Sounds like the disks need to spin up before the controller would recognize them. On a desktop system you load the kernel image from disk, so you are guaranteed that the disks are spinning before the kernel tried to detect them. Not so on the empeg, the kernel there is in flash. That's my understanding of it, anyway.
Borislav