On the Intel Motherboard there is a green light that stays on all the time when the power is on, and for the red led it is the onboard status amt led which stays on as well, it is for the Active Management Technology. On all Intel AMT Board, there is an AMT led.
Usually if the temperature was over-heated, the system will shut down automatically. To monitor the CPU temperature, you check it in the BIOS (hardware monitoring) or install the Intel Desktop Utilities which is available to download from the Intel Website.
If you are not using the AMT features, disable it or restore the AMT to default by changing the configuration jumper to Configuration Mode. For more information on AMT, go to the support page of the board , there is a section for Troubleshooting AMT.
One more thing to do as well, Go into the bios, Security Menu, Disable Chassis Intrusion if enabled as a precaution. :-)