Vision tool rotation on batch runs

Vision tool rotation on batch runs

I'm running a small, circular spacer part on a VMA-2520 (no probe) and having difficulty successfully running the parts in a batch. As more parts are completed in a batch run the vision tools of various captures seem to be picking up rotation and not capturing the features correctly.
I have the parts laid out on a 1" X 1" grid printed on a transparent vellum sheet so they are evenly spaced.
There are 800+ parts that need to be run so any help figuring out a way to get batch runs  working would be most appreciated.

Program:
  1. Image recognition is used to pick up 2 small cylinder bosses (.040 OD) as points
  2. Origin set to one point and aligned to the other (CAD alignment is set up with this configuration)
  3. Plane measured and leveled to
  4. Cad synced
  5. Various features are measured: Diameter of the bosses, a center bore, a datum feature and the outer diameter for a profile.
  6. Datums are aligned to
  7. Reports generated for features, positions and a profile.
Side Question: is there a way to set up the program so a batch run does not change the starting coordinates? Currently I have to reload the program and choose not to save.