It seems it is correct and the error is my brain and Mach3's tool path display.

So far all my work has been done in Q1 which is pretty normal and has home at bottom left corner, the work on the reverse side is in Q4 with home at top left - this seems to make the tool path display hang it off the bottom of the screen which made me think it was wrong.

I sketched out the four quadrants and pencilled in the first few G-code lines and they do indeed fall where they should :)

I will have a play on the machine tonight and do a dummy run.