Ok what kind of breakout?
If you have a volt meter disconnect the port cable from the breakout and you will likely have to change the active state of the E-Stop in Ports and Pins, Inputs to Active Low.
Next put the volt meter on Pin 1 and Pin 25 and jog the X one way then the other, does the voltage change between 5v and 0v depending on jog direction? If yes then check between pin 2 and 25 and jog again, does the voltage show a slight change as you jog?
If yes then it would seem the port is outputting correctly.
If no to either then remove the cable and check directly at the computer port and repeat the checks above.
Hood