If it is definitely the same profile you have opened then the only way to find where the problem is, is to start checking with a voltmeter or better a scope.
Using a volt meter you can start at the Dir pins on the parallel port itself and connect the voltmeter between the Dir pin and one of the Gnd pins of the port, jog that axis one way then the other and you should see the voltage change between 5v and 0v depending on the direction you jog. You can then move on to the rest of the system checking things if the port looks ok.
Hood