Several GIS programs, such as QGIS, internally use ST_Force_2D to make a 2D drawing from higher-dimension data types. I'm not sure how Mapnik treats these geometries, but I suspect they might not be supported. Also, be sure to double-check the extent, since this is often overlooked.
If you are not actually using the higher dimensions, then remove them! For PostGIS 2.0:
ALTER TABLE my_table
ALTER COLUMN way TYPE geometry(MultiPolygon,900913) USING ST_Force_2D(way);
And for PostGIS 1.x, see this answer.