I just "offlined" the system and took a look at the BIOS. The hard disk controller was set to "ATA NATIVE", I attempted changing to AHCI and the system failed to boot thereafter.
do you have ahci and ada drivers compiled in?
Booting into my rescue CD of FreeSBIE, with AHCI enabled only showed "ad4" (the troubled disk) to be registering.
showing up some, but not all disks after rebooting is quite common to the problem i described.
POWERING OFF (by disconnecting electricity, not by power button), waiting a minute, and powering on "fixes" the problem for some time.
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