I have an ESRI shapefile in WGS84 and convert it to another with a European Albers projection (EPSG:102013) with ogr2ogr.
ogr2ogr
ogr2ogr -f \'ESRI Shap
Already found the problem. I had a topojson.mesh layer with class .country-boundaries above the country layer, and this mesh had still a fill color defined. So I had to set
topojson.mesh
.country-boundaries
.country-boundaries { fill: none; }