Louis - what you need to do is find out where the problem is.
I will assume you have your steps per inch/millimeter properly set, your acceleration is reasonable etc. I assume that both your X and Y motors are set to the same settings as each other.
What you need to do is check the X axis motor and make sure it is all working correctly. If it is, then, without altering any settings on Mach 3, change the four drive wires on the motors - i.e. run the Y axis motor from the X axis wires (nothing else needs to be changed). Turn to Mach 3 and jog the X axis, the Y axis should move. Put commands in the MDI line for the X axis, the Y axis should follow exactly.
If the Y motor does not operate correctly, then the fault is a mechanical one with the Y motor, or the slide etc of your mill. Check it for smooth operation, and make sure th gibs are not too tight.
If the Y motor works correctly, then connect the X axis motor to the Y driver wires, and check that (using the Y jog and controls) - see if that works. If it doesn't, the the fault is in Mach3 or the driver.
If you can, change the wires from the LPT1 socket to the drivers - X for Y again, and try running the axis. If the fault is on the same motor, then it is your driver, if the fault has changed, then the fault is in Mach, probably with the settings. (If you cannot physically change the wires, the reassign the wires on the Config/Ports and Pins page, this will have the same effect).
I do not know the Hobbycnc product, and how much choice you have about wiring it. If it is all prewired, then you cannot do much else. If it is not prewired, then you can use different pin outs to drive the axis, to check all the pins.
I can't go much further at the minute until you post some results.