Thanks Hood, I have managed to check pins 3,4 and 7 which are the direction pins for X,Y and Z axes and all 3 behave the same way, ie. 0V for one direction and 5V for the other.
The board I am using is one I got off of ebay from China I think, which looks great as it will do all 3 axes, limit switches, E stop etc. all on the one board. I think, however that the problem must lie on the board, but wouldnt know where to start looking for that one!!
I have sent them a message asking for help, so hopefully I will get a solution from them, unless you can think of anything else I may have missed?
Tony