I think there are two leds on this motherboard. One is for power status which should always be green and the other one is the AMT led with may be green or red depending the status of the on-board AMT. If this light is red and you are not using AMT then it is normal. You do not have to worry about it.
If the fan is on and off after sometime continuously, they it may indicate something wrong with the processor.
Please check that the processor you are using is compatible with the motherboard:http://processormatch.intel.com/CompDB/SearchResult.aspx?Boardname=DQ45CB
Check if the processor is not faulty by testing it onto another compatible motherboard or to test another processor on the DQ45CB.
Check if the power supply is powerful enough, also try to test the system out of the pc case just to make sure there are no short circuits. Do these test with only processor(and its fan) and power supply on the motherboard and you should get 3 beeps.
Hope this will be helpful to you.
Let us know how it goes.