Re: PCB GCODE zeros of top and bottom layer don't match!
You don't get the origin to be bottom left for both sides! Try this, take a 3x5 card and lay it on the table. Put an X in the lower left corner (we will call this the top side).
Now flip the card on the Y axis and where does the X land (hint it will be on the lower right side)! You need to learn how to use fixture offsets.
I mill my top side on G54 and the bottom on G55! Yep, the origin is on the bottom left on the top and bottom right on the bottom. This way, I am flipping my board in the exact same space. To do it the way your looking at it, you will be strictly in G54 and the origin point has to be at the exact same location. This will require 2x the space to hold the board.
Art
AKA Country Bubba (Older Than Dirt)