I just installed my second new S1200BTLRM motherboard. I am interested to find out what is the reason for blinking amber status led. No other led are on/off/blinking. I didn't have this kind of result with my first motherboard.
I have upgraded firmwares to the latest. I also run sysinfo-tool which informed the following:
Boot Code: 02.02.00.049
ME Health Status: PSU MONITORING SERVICE ERROR
ME Health Status [Extended Information]: PROBLEM WITH PSU NO :1
BIOS error page didn't inform anything. Although I changed the psu, but the blinking didn't stop. The both PSU are conformable to ATX standard.
I am adding the following box to provide examples of possible causes of a flashing amber LED. You may find more information about the Status LEDs in our http://download.intel.com/support/motherboards/server/sb/g84364004_s1200v3rp_tps_r1_3.pdf Technical Product Specifications.
In this case, I would recommend running the most recent firmware release https://downloadcenter.intel.com/Detail_Desc.aspx?DwnldID=24418 02.02.0005 (it requires minimum BIOS update https://downloadcenter.intel.com/Detail_Desc.aspx?DwnldID=23859 02.01.0002).
If the issue remains, please contact http://www.intel.com/p/en_US/support/contactsupport Intel Customer Support for proper follow up.
I found out that the BMC was monitoring all fan headers and it was missing one. After I installed one fan more, there was no blinking amber, just solid green status. :-)