I think the Empeg is not giving enough time for the 2nd hard drive to spin-up before it checks for it.

Aha. Good catch!

From the Drive Upgrade Guide:

Another possible compatibility problem is if there's an extreme difference in spin-up time between the two drives, it might cause the second drive to time out if it takes too long. So you may want to consider installing your drives as a matched pair. This isn't strictly necessary, and if you're lucky, you might be able to work around these kinds of problems simply by swapping the drive order.
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Tony Fabris