What are you using as your reference for the voltage measurement? The optical sensor output goes HIGH (towards +3.3 V) when illuminated, so I wonder how you’ve connected it. The connections are:
Pin 2 - (Red wire): +3.3 V
Pin 5 - (Black wire): GND
Pin 6 - (Blue wire): OUTPUT
[Edit] As far as I’m aware, the sensor output is definitely not TTL, and should not have an external pull-up or pull-down resistor, so you should not be using a pull-up resistor inside the RPi.
Bear in mind the LED on the back is not a reliable indication of a change of state of the output… See First try with EmonPi - Pulsecount stuck at 1 - #16 by Robert.Wall