I was originally thrown by the flip flop output at TP5 being inverted, that was a symptom not a cause (pic 3), this was due to the reference voltage being shorted out and that resulted in the flip flop turning on both halves of the flip flop at the same time, as you can see in the attached image, which shows Q25 and Q27 base's both turning on at the same time ! (pic 1)
I traced this down by (unfortunately) cutting a track that feeds the reference to the flip flops and injecting my own supply to isolate the reference, that instantly corrected the flip flop fault, but the units fault was still present.
I then traced the fault back to the voltages on the collectors of Q19 and Q20, which were very different from each other, despite being mirrored circuits ! it turnout out that Q20 wasn't fully turning on to output -11VDC, and so it was never turning the JFETs off, this is what was shorting out the reference. (pic 1)