Ok The basic quadrature encoder has two square waves, displaced by 90° (quadrature) , originally the simple usage was to use one rising edge as count (basic count/rev) the other pulse the direction, soon it was observed the resolution could be increased by either using two of the rising edges of the pulses (x2), or every rising and falling edge (x4).
So this became the most common way of increasing the basic count resolution if desired.
What you have is a basic 1000 count encoder that the either the drive or the system takes advantage of the x4 capability, BTW Mach CNC does not count the pulses as the control is not closed back to the Trajectory planner as it is in commercial CNC or motion card etc, but is the responsibility of the drive to use the x4 to increase the resolution and track position.
Al.