Find why Indigo NoSQL and Bingo gives different number of search results

The presentation at http://www.slideshare.net/NextMoveSoftware/substructure-search-faceoff
on slide 20 for the same database and same search query shows different number of search hits for Indigo NoSQL (498,427) and Bingo(500,865). The search query is simple enough to expect that the number of hits should be the same. Database is available from here https://www.emolecules.com/info/plus/download-database
It is necessary to reproduce this finding and confirm that the number of hits is different. If this is the case, it is necessary to find a reason and if this is a bug, fix it.