Amber light blinking on Intel S5000VSA with Intel Chassis SC5299DP

Ok I have just built this server with the following:

Intel S5000VSA Motherboard
Intel SC5299DP Chassis

I was having some very noisy fan issues so I ran through all of the steps in this article to fix the problem.
After the FRU/SDR update the problem with the fans stopped.

The fan issue is now resolved however I still have 1 more issue that is causing the amber light on the front of the server to blink. I used the SEL Viewer to lookup what might be causing this and I don't understand what the error message means or what to do to fix it. I have found a few suggestions online to update the FRU/SDR again but I already did this and this is how I fixed the fan problem. I looked through the BIOS and can't seem to find anything either.

In the SEL it is listed as a CRITICAL EVENT and I have pasted the error as follows:

Num :  1736

Time Stamp :  01/05/2010-18:58:36

Sensor Type & Number :  Voltage /BB +1.2V Vtt (#0x10)

Event Description :  CRITICAL event: BB +1.2V Vtt reports the sensor is in a low, critical, and going lower state.  Sensor reading: 1.0962 Volts.  Threshold value: 1.0962 Volts.

Generator ID :  BMC - LUN #0 (Channel #00h)
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Did you update the BIOS and BMC before you updated SDR?

There is only one +1.2V Vtt on the board.
It is the FSB & CPU Vtt.
- see pic.

i would contact intel with this problem; it looks like a voltage gets too low - can be ram or others
can be a bad motherboard, or even PS
or check these pages out :
from that chart -  : bad PS rail (too low) or voltage regulator =  bad mobo
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qbarat2Author Commented:
I don't remember the particular order I did them in, but I updated all 3, the BIOS, BMC, and FRU/SDR. If you feel there is a specific order I need to do them in I can try if you think it will help.

Since I don't have another motherboard or memory to test with, I am going to try replacing the PS today, I will let you know how that goes.
I'm not sure if it will matter but the order I've done it in is BIOS, BMC, and then FRU/SDR.

I doubt the PSU is the issue for a few reasons:
1] Vtt is usually a single IC chip POL [Point of Load] regulator and they normally have a wide input range like 3.0v-15v or 5.0v-15v. Even if it's more complicated regulator with a Controller IC and MOSFETs then either: input range is going to be wider than the ATX +12v range spec -or- the system will shut down when +12v goes too low.
2] The Vtt regulator is powered from +12v and on this particular board it comes from the same PSU connector that provides +12v power to the VRMs for them to create the Vcore voltages. - Though it could with some abstract problem [like a failed Diode or something], I doubt +12v is going low enough to cause that warning without Vcore going out low too or causing the system to shutdown on low voltage.
- You can check the +12v at the connector with a multimeter. [It's the 2x8-pin "CPU Power" connector.]
If +12v -IS- low then you might have a bum [shorted] fan 'stealing' all the 'juice' before it gets to the Vtt regulator.
A bum fan would also explain the fans running too fast which is what started all your problems.

~~~ I think this is most likely the problem.
Perhaps the defaults on the reloaded BIOS and firmwares simply set it wrong and you need to manually set them.
Installing things in the wrong order -might- create that problem out of the blue. [Why I asked.]
I don't remember for sure if there is an adjustment for that voltage in the BIOS but -I think- there is.
qbarat2Author Commented:
Thank you very much for the chart, it gave me a good idea of where to start. I fixed the problem by updating to the latest SDR, however this caused the fans to start spinning loudly again. So the original problem returned. The reason the fans were spinning at max speed was not a software issue but a hardware one. Apparently this issue is casued by third party fans, (I was using Dynatron fans). After I replaced the CPU fans with Intel branded fans, the problem instantly corrected itself.
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