I've got it working!
It did a clean install and followed the instructions directly but ended up in the same place. So I then went through and switched some wires around for example to use the X axis channel to control the Z drivers and motors just to double check the drivers were still working. In doing so I noticed that the strange behaviour on one of the axis with pressing the jog in either direction button resulted in the motor being driven in the same direction regardless. So then that made me suspicious that even though the behaviour was very weird - it could be a wiring problem. There was one wire that had come loose on the X axis driver. So in the end I think it was actually just one or more wiring problems that resulted in some strange behaviour that looked on the face of it like a config. problem.
Thanks for all of the help.