@dutti Glad it's fixed - I thought that would do the trick.
"Jerk" is an odd term as applied to 3D printing - that's why it's referred to as instantaneous speed change in RepRap firmware. But technically, there is no such thing as instantaneous speed change - it is physically impossible, so lets stick with the term "jerk".
Without such a setting, every move would start from a speed of zero, accelerate up to the required speed, then decelerate back to zero speed. But curves are made up of tiny segments of individual moves so if the print head had to start and stop for each of those tiny segments then the overall speed would be very slow. Hence we use "Jerk" which is the speed threshold that one move ends and the next one starts without coming to a complete stop in between each move.
Extruders are treated like axes so every move comprises XY and E (and maybe Z as well). Those XY and E moves all have to be synchronised so that they all start and end at the same time. So with a very low extruder "jerk" setting, the extruder has to slow right down at the end of each move but because X and Y have to be synchronised, they too have to slow right down to keep them synchronised. That's why you had the problem.