Okay, so the pendulum of blame swings from BOB to PC.

Now that I know that you're happy patching pins on the parallel port, lets test the actual machine.

With all cables/ribbons on the Syil in place, from the DB25 on the machine (not the PC!), ground the X-Axis "Step" pin (pin 7 to pin 25). I'm assuming here that the pin is pulled high on the BOB. At the point that you ground the pin 7 you should get a single step on the x-axis. Continually breaking/making that connection should introduce further steps. The machine isn't going to launch itself - just move microscopically in one direction on the X-axis.

If that's the case then I think you need to look at the parallel port set-up.