DL380 G4 with Smart Array 6400 and 6 drives

[CA1188698]

We are trying to configure a Smart Array 6400 in a DL380 G4 with multiple drives have 2 configured arrays.
The drive configuration is *2x146GB HDD's connected to the on-board controller and 4 x146GB HDD's connected to the Smart Array 6400.
*The OS is Microsoft Server 2003 installed on the first array which is working flawlessly.

Problem: The 4 drives attached to the Smart Array 6400 are seen but by the controller but are not configuring to an array correctly.
This is proven by toggling each HDD LED via the Smart Array 6400 BIOS setup. In the fault condition only 2 of the 4 drive LED's will light when selected.
In a known good working condition, all 6 drives (connected to one controller) on either the on-board or the smart array controller, show each drive LED when selected.
The faulty LED HDD indication positions are on the LH side looking at the server from front on.

We have tried, with no success, the following and in most cases combined configurations:
All current BIOS levels
New Smart Array 6400 controller
Swapping physical disk positions (fault remains, does not follow drives)
Different Smart Array 6400 SCSI Port
New Smart Array 6400 SCSI cable

We have not tried a new SCSI terminator as the first array is working fine.

Can anyone indicate where our problem may be?

[CA859951]

This is a brand new server, you should warranty replace the backplane board. If you cannot get response from the drives in a particular spot, it has to be the backplane board.

SCSI backplane LVD, six-bay - Spare part Number 359253-001

G'luck! -john

[CA1188698]

New Backplane gives the same fault condition.
After further diagnosis by using the drives configured on both on-board SCSI ports but separate arrays, it appears the 6400 controller (firmware) it at fault.