Machine Stutter / Notching Phenomenon

It was, there was one line per axis:

setp parport.0.pin-02-out-invert 1
net xdir => parport.0.pin-02-out
net xstep => parport.0.pin-03-out
setp parport.0.pin-03-out-reset 1

setp parport.0.pin-04-out-invert 1
net ydir => parport.0.pin-04-out
net ystep => parport.0.pin-05-out
setp parport.0.pin-05-out-reset 1

setp parport.0.pin-06-out-invert 1
net zdir => parport.0.pin-06-out
net zstep => parport.0.pin-07-out
setp parport.0.pin-07-out-reset 1

Someone on the facebook page has since said that i actually need these lines but to increase the reset timer?

I have no idea what these lines are for, from what i can tell something to do with double stepping?

This line from your hal file sets the step pulse length:

setp parport.0.reset-time 2500

I would try setting this to 5000 and see if it makes a difference