NCBox Parallel port not right

I have a something strange going on with the parallel port on the NCbox. I've attached 3 scope pictures. No control of the motors.

I currently have the scope looking at pins 2 and 3, and 0V pin 25. The my-mill.ini has pins 2,3 set to X step, X Dir. Current LPT is set to 279, the D shaped one on the NCbox.

LinuxCNC start shows the wave form on the LPT as Linuxcnc starts up. OK nothing looks too strange here. I remember the mill motors coming on line before with a slight hum.

Now if I enable it and use the manual controls to move the X direction + & - I get the X Going Left and X Going right. These look identical, but I am sure they are not supposed to be. (Sorry they are blurry - typical iPhone pictures with one hand ) but you can make out.

Now the really strange thing, if I click on the Y in manual control and use the + & - I get the same wave forms, same happens for the Z, and I have not changed the pins I am monitoring on the scope.

Any ideas?
Col