I have had the same problem with the Germany extract from Geofabrik (the Bodensee and part of the Rhine was empty). Caused by incomplete multipolygons at the border regions due to the cutting. I download those complete relations with overpass and add them to the germany-latest.osm.pbf with osmconvert: %DIR%\tools\wget.exe "http://overpass-api.de/api/interpreter?data=(relation(1685222);node(r)->.nodes;way(r);node(w););out meta;" -O "%DIR%\resources\rhein.osm" %DIR%\tools\wget.exe "http://overpass-api.de/api/interpreter?data=(relation(1156846);node(r)->.nodes;way(r);node(w););out meta;" -O "%DIR%\resources\bodensee.osm" %DIR%\tools\osmconvert.exe --drop-version %DIR%\%date%\Splitter\germany-latest.osm.pbf %DIR%\resources\rhein.osm %DIR%\resources\bodensee.osm --complex-ways -o=%DIR%\%date%\Splitter\DE.o5m