I've got a file server that's using an Intel S5000VSA sever board with Intel Embedded Server Raid. Have six Western Digital Caviar drives plugged into it. (I have a couple of these units, actually.) BIOS level is 8.00.10, and RAID driver is at 126.96.36.1997.
I noticed that on one particular unit, the "plugged in" LED is not lit on four of the six drives. The activity LED still works and blinks away when the drives are in use. I'm not seeing any errors reported in the RAID Web Console or in Windows events.
Any way to know what is causing this?
The LED behavior may relate to the backplane, the controller and the disk. What chassis/backplane are you using?
If I remember correctly, on most Intel backplanes when you use SATA drives the drive LED remains off, while with SAS drives the LED is on upon drive presence.
Also, your BIOS and driver version seems really old, although the BIOS string you provided is not complete and I can't tell exactly which version it is. Check http://downloadcenter.intel.com/Product_Filter.aspx?ProductID=2487 for updated BIOS/FW/driver.