You are running the drives as individual disks (right?) so I don't think disk geometry would be causing this problem. I have read that the DNS-323 format process writes disk serial number to the system flash. There is a possibility that during the up/down grading and formatting, these values in the flash and the actual drives are not consistent and triggering the failed drive alert.
My only suggestion at this point, would be to "start over" and setup the DNS-323 to v1.05 again.
1. Backup the data
2. Delete the partitions from the drives
3. With no drives installed, flash the DNS-323 with fw v1.05
4. Install both drives and format as individual drives
5. Restore data
I know this is a "sledge hammer" approach
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, but I can't think of anything else other that just use fw v1.04.