Ok the G28Z0 line is telling Mach to go to Home position, are you homing with Z fully down?
Hood

Do you have different lengths in the tool table that would cause different offsets with the G43?

I found it, there seemed to be an issue as there where zero Z was.. Even though I had set the zero points by clicking Zero X Zero Y Zero Z I needed to click REF ALL HOME for it to look right.. I don't quite understand why that is exactly but it's milling now and that's really all the matters!

Thanks for all your help though, no doubt I'll back on here when I try to get all that 3D printing stuff bolted to it next week.

It is because you never homed so Mach thout the machine zero was way down and the G28Z0 was sending Mach to machine zero.
Hood

I have megnetic switches in -X -Y and +Z, is there an auto homing function to use these? That's hat my previous package did.

You just set them up in Ports and Pins/ Inputs to whatever port and pin you have them connected to.
Hood