Z-axis not working on lathe & mill

HI
I am in the middle of converting my CNC Lathe & Mill setup from WinXP/Mach3 to Ubuntu12_04/LinuxCNC 2.7.14 using the Axis interface.
The two machines are using separate HobbyCNC Pro Chopper Driver boards - one 2 axis, the other 4.
This is a retirement project after spending the period 1980 to 2000 installing , writing and testing Unix systems and software.
I have found a way around most of the problems it has thrown at me so far - don't ask, the answer would be too long.
Everything worked fine in the previous Mach3 setup so I used all the settings from there, manually transferred into Stepconf.
Two problems have got me stumped.
First - I cannot get a response from the Z-axis on the mill when testing with stepconf - X, Y & A work fine.
I have tried inverting step and direction for the Z-axis pins in all possible combinations with no effect.
The Z-axis values are the same as for the X & Y axes, apart from shorter "Table" travel length.
All leadscrews are the same pitch.
Secondly (and even weirder) the lathe Z-axis is fine in stepconf but refuses to respond to MDI commands in LinuxCNC.
The DRO changes, but not the machine.
Any possible assistance would be greatly appreciated.

Thanks for the reply.
I have now nailed down the problem - hardware not software.
Specifically a parallel port cable problem. With 2 controllers to run from Linux, I first tried 2 parallel port cards in my PC.
A long PCI card plugged into the long PCI slot at 0xec00 and a short card in the shorter PCIExpress slot.
My ASUS M5-A88-M EVO MB does not have an on-board parallel port, not even a header for one.
Linux can see the long card, but not the short one.
Tried many ways to find the address for the second card. Gave up and dug out an old parallel cable switch. The latter checks out
fine for continuity, but it seems to be the cause of the problems. Plugged each controller cable direct into the one working port
and all works OK. Now I need to find a way to get the second port card working so that I do not need to switch cables when I
switch machine tools - any ideas?

Yes perhaps that may be quickest - the only problem is finding one that works.
Found this - Syba PCIe 1 Port Printer/Parallel Card Moschip 9901 Chipset
Uses the same same chipset as the one that is working on my PC, also claims to be Linux compatible.
Anybody out there actually using this one? It would be good to get confirmation it works as it is not cheap.