I then checked each pin of the parallel port to make sure it was get the necessary voltage and it was.
How did you test this?
The easiest way is to jog an axis back and forth, and measure the voltage at the direction pin.
It should be 5V in one direction, and 0V in the other direction.
My guess is that your port address is wrong, or the port is not working properly, assuming nothing else has changed.
An alternative to a PCI port would be a UC100 motion controller, which in many cases can be easier than getting a PCI port to work.