With the input from you guy's I think I have managed to solve the issue, I have sped up the acceleration (I tend to be very conservative) and turned on the CV with appropriate feed rates, and all seems to be working ok now.
I still couldn’t find “Simulation” under Motion Devices, see attached image, I assume I have somehow made it disappear when I created the Profile I use, because it is available in the standard MACH4 Router Profile.
I also assume the WARNING about “Changing the motion control device will destroy any existing axis motor mapping and motor tuning".
If I did use the Simulation Device would the axis mapping and tuning still be in the PNDX Device when I went back to it?