Rather than just changing the threshold for one of the sensors I wanted to use a more general solution, not least because the four sensors I have share the one comparator circuit. The sensor I am using is an SG-2BC, it looks fairly similar to the CNY70. On the axes that work, the output goes from ~<1V for a "0" and ~4.5V for a "1". The problematic one gives around 0.5V up to ~2V. By putting a shroud on the sensor and darkening the are around the grub screw on that particular shaft, I have gotten the output to give a value >2.5V. I was hoping for a more elegant solution. I've already replaced the sensor and I'm satisfied that there are no electrical problems in the system.