Parity sync only using drives on SAS1

CPU: Intel i3-2120 (3.3GHz)

Motherboard: Supermicro MBD-X9SCM-F-O

Memory: 8GB Kingston (DDR3 1333)

Power Supply: Corsair AX850

SAS Cards: 3x Supermicro AOC-SAS2LP-MV8

Hard drives: 12x 2TB Western Digital Green (WD20EARS), 8x 3TB Western Digital Green (WD30EZRX)

Unraid 5.0 RC4

Just built this, started up unRAID, all drives were green still. So I started the array, then I started a parity sync (with correct unchecked), and this is what happened. It only used the drives on the first SAS card and the server became unresponsive. I noticed that the first SAS card is not scanned on boot unlike the other two.

What's going on? I am unable to get a log. I disabled INT13 on all 3 cards.

Called Supermicro and the guy told me to update to BIOS 2.0a (released a few days ago), and set PCI-E slots OPROM to disabled.

Seems to have fixed this.

EDIT: It was not the BIOS update that fixed it, but the disabling PCI-E OPROM for all slots.

I have a very similar system to yours. 

Neither disabling ROM boot nor Int13 did resolve my problems with those cards. But changing the motherboard from Supermicro X9SCL+-F  to X9SCM-F did.

Do you have the link to the updated firmware? It is not referenced on the product page yet: http://www.supermicro.com/products/accessories/addon/AOC-SAS2LP-MV8.cfm

There is an updated Linux driver there though. Wondering if that will improve anything.

I am having trouble with my server and expect it may be my AOC-SAS2LP-MV8.

When I run a parity check, I lose connection to one of the drives on the AOC-SAS2LP-MV8 and it red-balls.

1.  How do I disable PCI-E OPROM for all slots, I assume this is in my motherboard BIOS, I don't use a SM board but there might be a similar setting?

2.  How do perform the BIOS/Firmware upgrade?

Thank you!