Brian, I guess where you might be left at for options is to revert the firmware to 1.01 and see if that helps, it seemed to work well for some other members of this forum.
But before you do that, the only other thing I would ask is, do you have enough storage space on other drives to empty the original drive and let the 321 format both and turn them into RAID drives? I know it's asking a lot, not many have an extra 1 TB of storage space lying around. I do, so that's why I ask. If you can back up the data and the config file then you should be able to try to get the 321 to format both drives and RAID them, and if that fails, swap them into the opposite slots and try again. The reason I suggest this is that, when I built my 321 RAID 1, I used 2 empty drives and all the 321 did was tell me that it was going to format the left drive and that all data would be lost, and did I want to continue. And since that day my 321 has been working like a charm, no problems, well...except for the auto-power up issue.

If that all fails, then I'd be reverting the firmware to 1.01 and giving that a whirl. At that point, what have you got to lose, with everything backed up and safe.
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Good luck dude, I sure hope you solve this majorly perplexing puzzle!
Ryder