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Intel Server Forgot RAID Configuration

A customer called and reported that a server could not start up and the error message was regarding missing NTLDR.

Arrived on site and checked the server, which is in a secured location with no physical access except to a few trusted employees, and found that its RAID configuration was lost - all 4 drives showed READY instead of (for example) ONLINE-A00 .

I reconfigured the array back to its original state (4x500GB HDD's in a RAID 5, no HS) and it booted into Windows more or less normally albeit slowly.  I checked the Intel RAID web console and found my array is performing a background initialization.

When I disabled IPSec and rebooted the RAID controller lost its configuration again and the RAID must be reconfigured by pressing Ctrl+E during the RAID Bios display.

I can configure the RAID in the BIOS then restart without issue, even boot to a boot disk then reboot and maintain the configuration.  It seems to only be in Windows that this is occurring.

Intel S5000VSA Mainboard, Windows 2003 x64 Enterprise, Xeon CPU, server is just under 3 years old.

What could be causing this issue?

How do I fix it?
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Mazdajai
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Did the board has the latest firmware?

Link to Board Firmware:

Oprom Firmware for SAS Board:
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darnitol500

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One of the possibility that RAID controller lost its configuration is a faulty CMOS battery that holds the configuration. Replace the motherboard and let us know if the problem persists.
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darnitol500

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A  failed battery has been suggested, is the raid cmos battery replaceable?
Yes. It holds the time, date and other motherboard configuration.
I unplugged the server from ac for a few minutes and plugged out in and it held the date/time, can there be two batteries?
Unplug the server does not affect the battery. The battery is located is located on the center of the board.

You can download the manual here.
I think there may be a misunderstanding:  doesn't the battery help the bios keep its data while the server is disconnected from ac power?  Wouldn't a failed battery mean the unit would lose its bios configs (including date and time) when disconnected from ac?
That is a big misunderstanding.

BIOS settings are kept in CMOS, a nonvolatile memory. CMOS needs it own battery, which is CMOS battery. CMOS battery is designed to keep BIOS settings and independent with AC power.

CMOS battery usually last 7 - 10 years. However, Incorrect system date and time; loss of BIOS settings are symptoms signs of a dying CMOS battery.
Replacing the main board fixed it.