So after breaking a BeagleBone Black by putting 5v onto the breakout pin on the P8 side... we were supplied with a new one! (thanks!).
This meant that I could go back to coding for the scoring system. After working out the pinmux, from various confusing (inaccurate) sources and cross-referencing with the technical reference manual(s), for the mode and setting the pin for input, I had something which, when the infra-red beam is broken, turns a green LED on. I've created a nice spreadsheet which has the values in, which I'll post up later. Probably to Google Docs.
The transmitter and receiver are a little difficult to see on there (so, Drew, this is my setup!) and we're not using any capes or such, just plain breadboard and wires. Funnily I didn't find any examples of actually using the PRU to receive data on the pins, just output data on them. The simplest way to handle it, has been just to check if a bit has been set on that pin and then behave accordingly.
We also suspect that the Video4Linux drivers were playing havoc, preventing us from capturing high resolution video to do the ball tracking on the BeagleBone Black. Currently it's pretty low but seems to be sufficient for our image analysis to work, so that we have got nice direction prediction.