well my guess is still the cable. If you have an Ohm meter you can remove it and check continuity between the pins on either end.
Other thing you could do is connect the Z axis to the 4th axis output on the G540 and reconfigure it in Mach for those pins, thats assuming you are not using a 4th axis. Unfortunately that wont tell you if its the cable or the G540 though but it may get you running.
If you have a scope or a voltmeter you could start testing the outputs from the SS and then test at the end of the cable if they check out ok.
Hood