Dear George,
As reported in the Sen2Cor section on STEP website (http://step.esa.int/main/third-party-plugins-2/sen2cor/sen2cor_v2-8/), the only differences between “L2A Toolbox” and L2A generated at S2PDGS are reported in the following table:
I guess that the difference is due to the DEM used in the processing.
Best Regards,
Fabrizio