@pro lamer - I have multiple power supplies. I have tested two different ones and the computer crashed on both (600 watt), so I don't suspect it's the PSU. I have ordered two more (an 850 watt Gold) and I intend to wire the HDD's to a separate PSU that won't turn off, so if the computer crashes/reboots the HDD's will still keep spinning.
@Jailer My hardware is listed in my signature. I'm not sure I agree with your assessment because this happened whether I was using the Asmedia controller or the LSI controller.
Before I do anything else- I was thinking about buying 11 new identical HDD's and cloning the current drives to them. Is this possible? I was wondering if you could do a sector-to-sector copy (done by dd) in Clonezilla. Is this possible or does FreeNAS match an ID (gptid for example) to an HDD's serial number? If I can clone them- then I have no problem experimenting on the cloned drives until I solve this.