This:

   Node file = root.addNode(filename, "nt:file");

   Node content = file.addNode("jcr:content", "nt:resource");

   content.setProperty("jcr:data", in);

with in=InputStream (in fact this is a FileInputStream) works fine.

But this:

   Node file = root.addNode(filename, "nt:file");

   Node content = file.addNode("jcr:content", "nt:resource");

   Binary binary = session.getValueFactory().createBinary(in);

   content.setProperty("jcr:data", binary);

does not.

Reading the source code  it seems that the problem is in AbstractJcrNode.java:

    final JcrValue valueFrom( Binary value ) {

       ValueFactories factories = cache.factories();

        org.modeshape.graph.property.Binary binary = ((JcrBinary)value).binary();

        return new JcrValue(factories, cache, PropertyType.DATE, binary);

    }

DATE is wrong. No ?