Checking page 4 of the schematics, the red power LED (D6) is connected via 1K resistor directly to the +3.3V rail. It is not controlled by the CPU or any other circuit. So, if that LED is blinking, it means your 3.3V power is turning on and off. You've most likely got a broken connector, cable, or an intermittent short that is causing that. If it's the D5 green status light, then I think blinking indicates SD card access.)
http://www.raspberrypi.org/wp-.....s-R1.0.pdf