Have calibrated, calibrated and calibrated. Then I found out my calipers weren't zeroed properly (I use old school non digital calipers), and re did it all again. No dice.
So I gave up on the black PLA, and pulled some PETG I've had sitting in the drawers for a couple of months waiting to try.
Got the petg going nicely in calibration prints, barely more stringing than the PLA so I try to print the part that was causing me problems, but no joy, same issue! So I try again and sit down to watch it, and the skipping doesn't come from the peaks as I suspected, rather it is coming from some unreasonably high jerk settings I don't remember changing, the machine was literally trying to shake itself apart on small infill sections.
So I probably didn't need to abandon the PLA, I could have persisted and found this was the problem, not the retraction as I had assumed.
On the other hand I got over my 'fear' of PETG and this print is coming along very nicely!