UP DATE:
I think in my case I found the issue.
When I set up the layout in Illustrator, I placed the bounding box used to set the OPS corner marks TO CLOSE to a piece of the artwork. This resulted in the OPS system picking up this artwork, and interpreting it as part of the corner locating crop marks. I cut these extra pieces out on several of my pieces by hand to eliminate the OPS confusion, and WAH LA the plotter works correctly.
Lesson to self [and others] NEVER place artwork to close to crop marks.