It could be a problem with the a) splitter or the b) geofabrik abstract (because Lac leman is in two countries). Which splitter options do you use?
Maybe try the geofabrik europe.osm.pbf extract (pbf is smaller and works faster than the osm.bz2) with the splitter areas.list that you already have.
java -Xmx1024m -jar …\splitter-r170\splitter.jar --split-file=areas.list --overlap=6000 europe.osm.pbf