Which firmware was installed when you formatted the virgin drive for the first time? Formatting does not erase partitions. If the older firmware used to format the virgin drive created partitions which are slightly out, then they may not mount with later firmware, and reformatting wont fix it.
I don't remember, it was for sure in the 2.XX range. I'm aware of the differences between formatting and partitioning. What I can do is to mount the drive in the pc and check the alignment with Paragon Alignment Tool and report back. It could even be that I partitioned it first with Paragon and then formatted with the MED.
In any case a misaligned partition should just slow down read/write but still be accessible.
About the FW, I flashed the 3.0.4 when it was released, I skipped 3.0.5 and flashed 3.0.6 just a few days ago. When yesterday the drive disappeared I rebooted several times, every time I could hear the drive briefly spinning up and the spinning down again
EDIT
That was fast
.... Paragon reports the partition as aligned, no operation is required