Thanks MaJiG. I didn't reply earlier because I wanted the sun to set so I could have identical conditions. I don't have an op amp and getting new hardware is a pain that I 'm going to avoid for the time being.
The emitter / receiver are not one unit, they are a pair I got on a whim when I saw them at a local shop and thought I could play with. Now, some more cool stuff happened. I swapped the resistor and receiver so I could read across the receiver like you suggested. Measuring via DMM, I was only getting about half the value range I was getting last night. Weird, I d' have thought the only difference would be that the high and low values would have swapped. I swapped them back to the original position and again, I only get half the range. The emitting LED seems OK, I can see it glowing when I look at it through a digital camera and the current going through it is the same. When the sensor is at the GND side of the divider, I get a rough range of 4.5V to 2.2V (46% of the value range).
Now, the funny thing is that the measurement has started working when only the board is connected. With the DMM connected, I get a rough range of 970 to 470 from the ADC (49% of the value range). With the DMM disconnected, I get roughly 1010 to 500 (again, 49%).
Thinking about this makes even less sense. These measurements are with the receiver on the GND side of the divider. This implies that the high values happen when the receiver has a high impedance and the low ones when it has a low one. Which implies that overall, the value of my divider is higher than yesterday. Which implies that the ADC should be tripping things up even more brutally. However, all that happens when I disconnect the DMM is that the measurements shift up a tiny bit.
One more thing that I observed is that the range of the sensor seems to have dropped. I didn't really make any measurements, but judging by eye, I am certain I was getting a noticeable value change at a greater distance. I thought maybe the emitter has a problem but I changed it and still got the same results.
Anyway, it's not particularly important if I make this work or not (I 'm just fooling around with random components), I 'm mostly stumped by what I 'm observing which is why I 'm posting here from academic curiosity. If you have any ideas don't hesitate to share.