bobbya47,
You have me confused, one time you have 0-3.3 v another almost 5 v.
You never mentioned what you drive requires. But lets backup some....
-Mach will send the info to the PP for the pulses required.
-You have shown that there is a high and low voltage for the pulse. But you have also shown that is a difference between the pins.
So how about just getting only one axis to work with the pins that put out the higher voltage rather than playing with them all and making it complex. Once you have the one axis working you can swap that cable to the other drives and see if they all work. Then you have the setup which you know needs to be in place to get the others to work. You can add all the other stuff, like homing etc later.
What make drives are you using? Other than Gecko post info on them.
RICH