Thank you for your reply joeaverage
It is much appreciated. Yes, we have done the driver test within the mach3 folder and the system came back as excellent up to 75,000 KHz. I am then assuming that there are no problems there. OK, I will configure the Estop on mach3 using the conifguration menu on ports and pins but I think we have already done that, we enabled it and set the relevant settings. Thats the real problem we are having, access to the actual manual I have tried to get in touch with the suppliers many times and always I get the same response, everything you need is on the website. There's only a wiring diagram and a rar file for the mach3 setup which am not even sure is 100 percent correct. Two blue lights come on the breakout board so I am assuming that means good connection.
Can anyone think of any other reasons why the mach3 may not be communicating well with our circuit.