Didn't have time to read through every line but here
Don't know if this has been suggested, But your 12 Mil lam may need to be taken out of the equation to qualify the issue. 12 Mil could be creating an effect like viewing through a glass of water. The actual and read postion of the mark could be skewed. Roland crop marks are not the most accurate as it is. I would recommend putting stick it notes over all the crop marks/ Laminate, then cut out the notes so the eye of the machine can get the true print....Not the print underneath a mottled 12Mil clear.