As Andrew mentioned, we put the scope on the step signals from the UC300ETH (ie going to the opto-isolated breakout board), and also the signals output from the breakout board, while jogging the machine manually. Immediately it was obvious that there was some funny signals - small amounts of noise on the UC300ETH outputs, but more on the breakout outputs.
After a bit of pondering, I checked whether there was any noise with all axes not moving - and yes there was - a lot !! Noise (about +/- 1V peak to peak) on the UC300ETH outputs, being converted by the breakout board to full 5V pulses at 43.5 kHz !
Andrew suggested we disconnect the analog signal to the spindle VFD and sure enough, all noise went away, leaving a nice clean step signal.
Now it made sense why things got worse when the kernel speed was reduced. We had a fixed frequency of corrupted step pulses due to noise at 43.5 kHz, which becomes more significant when compared to the true step pulses as kernel speed was dropped from 400 kHz down to 200 or 100 kHz.
Thanks all for the hints and suggestions for troubleshooting. I think Andrew and I have both learnt a bit from this little problem
