Newbie at doing face 6 operations - nested based cnc router.

We are going to be machining some parts that need machining on both face 5 and 6.  We are planning on doing face 6 machining first, flipping whole sheets and then running face 5.  Machine 0 is at the lower left corner of the machine.

When looking at the g-code produced by Microvellum for the face 6 operations, it looks good until I look at the trim cuts.  The code shows it machining off the lower left corner, leaving the right side untouched.  That would mean when I flip a sheet and reindex at the lower left, I will not have a machined edge to reference and will not be accurate.  Shouldn't it machine off the right side instead so when flipped, there is a machined edge to reference?

What am I missing?  Is this a setting that I am missing some place?