Weird SDF output

foo.java

package net.sf.cdk.tools;

import org.openscience.cdk.ChemFile;
import org.openscience.cdk.MoleculeSet;
import org.openscience.cdk.exception.CDKException;
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.interfaces.IMoleculeSet;
import org.openscience.cdk.io.MDLV2000Reader;
import org.openscience.cdk.io.SDFWriter;
import org.openscience.cdk.io.listener.PropertiesListener;
import org.openscience.cdk.tools.manipulator.ChemFileManipulator;
import org.openscience.cdk.tools.manipulator.AtomContainerManipulator;

import java.io.FileReader;
import java.io.FileWriter;
import java.io.IOException;
import java.util.List;
import java.util.Properties;

/**
 * A one line summary.
 *
 * @author Rajarshi Guha
 */
public class foo {
    public static void main(String[] args) throws CDKException, IOException {
        MDLV2000Reader reader = new MDLV2000Reader(new FileReader("/Users/guhar/tmp/nci10_original.sdf"));
        ChemFile chemFile = reader.read(new ChemFile());
        List<IAtomContainer> mols = ChemFileManipulator.getAllAtomContainers(chemFile);

        for (int i = 0; i < mols.size(); i++) {
            try {
                AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(mols.get(i));
            } catch (CDKException e) {

            }
        }

        SDFWriter writer = new SDFWriter(new FileWriter("foo.sdf"));

        Properties sdfWriterProps = new Properties();
        sdfWriterProps.put("writeProperties", "false");
        writer.addChemObjectIOListener(
                new PropertiesListener(sdfWriterProps)
        );
        writer.customizeJob();

        IMoleculeSet molset = new MoleculeSet();
        for (IAtomContainer mol : mols) molset.addAtomContainer(mol);
        writer.write(molset);
        writer.close();
    }
}