I apologize if I am missing the issue, but one thing I noticed is your use of a MDF jig.
I use a jig like yours to complete milling on the second side of an initial cut, when I first setup this jig I was using MDF. Then in CAD, once I flip the parts the machine should know where the parts were, but the MDF was expanding/contracting meaning I was not getting the cuts that I wanted. Could this be your issue? The MDF jig you have at the bottom of your stack may not be perfectly square due to moisture making the MDF expand/contract?
To solve this, I am using a jig that was cut out of aluminum. I was getting cuts that were off by 0.1 mm to 1 mm, due to my MDF jig expanding/contracting.