Hi Irving thanks for the reply.

The Kernel speed is set to 35KHz the same as before, I have tried changing the pulse width but only on the Z axis I will go and give it try on all axis and saving the XML.

One more thing I have noticed is the Home LED's on the MACH diagnostics screen, when my home switches are made they are flashing randomly but the LED's on my breakout board are solid and the home switches work fine?