Why do Polyphen-2 prediction scores differ when generated automatically versus manually? 

The Polyphen-2 prediction scores automatically displayed in AlamutTM Visual Plus are extracted from the WHESS database (http://genetics.bwh.harvard.edu/pph2/dbsearch.shtml). The WHESS database contains a pre-computed set of PolyPhen-2 predictions for the Whole Human Exome Sequence Space. 
Whereas, the scores obtained on the site using the batch query (http://genetics.bwh.harvard.edu/pph2/bgi.shtml) are generated upon each request.