A defect caused Bentley Map Enterprise V8i (SELECT series 4) v08.11.09.615 to create two shapefiles when the feature was inferred rather than native. The workaround is to use the Add Shapefile Directory option rather than Add Shapefile when setting up your Export parameters.
This issue has been corrected in Bentley Map V8i (SELECTseries 4) 08.11.09.838 and above