For those three pictures on the axis settings - I'd be setting the pulse-width to 5us in the first instance. The reason? - okay, I don't know what stepper drivers you're using but many/most use opto-isolated inputs for the step/dir signals, and /cheap/ opto-isolators can have slow response-times in the order of 3-4us (actually, worst-case performance can exceed 5us on many devices). Some are faster, but typically cheaper devices are relatively slow. Changing the pulse-width to the slowest possible (5us) gives the best possible chance for the pulse signal to be recognised by the stepper driver.