With the same box query against the same shapefile if rendering via the OGR plugin less features are queried than the shapefile driver, but with the same visual result.
Test added to confirm this: https://trac.mapnik.org/changeset/2981
[springmeyer] discussed with artem that this is likely due to our handling of multigeometries. We can improve and optimize. The task here is to augment the shapeindex tool to introspect shapes, split each geometry and add entries for each component bbox into the spatial index.
comment test for now - refs #783
not important to fix