@StephenRC:

Check the M350 line, the configurator has an error. It thinks there's only the X axis.

It outputs:
M350 X16 X16 X16 X16 I1 ; Configure microstepping with interpolation

Corrected version:
M350 X16 Y16 Z16 E16 I1 ; Configure microstepping with interpolation

Actually, unless you change it in the configurator, by default it outputs I0 at the end (without interpolation) so it needs to be changed to I1 as well.

Ian