Thanks Jake, it turned out to be just one step that made all the difference. After completing an action once, I just went to pull-down list of: geoprocessing\results and then right-click on the process that I had just completed, and copied as python script, then pasted that command line into a python script that I had written to batch process layers. Given that I had seven different steps using 40 layers, with some steps seeking intersections between layers, this saved me a few days work.
