Ok, so I had 100 of these to do, and I worked on them 8 hours today, and knocked them out after lots of trial and error. From what I can tell, the thick laminate caused my print to not lay totally flat when the eye was trying to read the crop marks. It had nothing to do w/ the laminate being over the crop marks, because I did it this same way, didn't put new marks on, and just had a solid sheet of laminate on top of it. I ended up having to just hold my finger next to the reader as the media advanced and it was looking for the crop marks. If I did that, it worked every time, if I didn't...it wouldn't ever work. Crazy the amount of stuff I tried, but never had an issue w/ media being this "wavy".
The other problem was I had the blade sticking so far down, that as it would advance around the sheet, it was dragging the blade across the graphics. I also realized that these did need to be cut twice to get anything accomplished. Since I had already printed them all, there wasn't any going back and modifying the file to tell it to cut twice, so I essentially had to stop it mid cut and pull the blade out after each row of graphics, and then run again. So to finish a sheet of 10, it involved stopping the machine 8 times and inserting/removing the blade, since I had to go back and tell it to cut it all twice.
I had to do one reprint from the first print trying to get the blade depth correct, and so in the reprint, I gave it two cut lines, and it worked awesome.
It was a crazy learning experience, but I learned a lot, and made money in the process.