The code in D3DSwapChain.java does not handle dirty regions correctly for at least two reasons:

1) does not use the passed in clip to reduce the region rendered
2) does not switch to a SRC style copy (not SRC_OVER blending) which is needed for a transparent stage.

    public void present(Rectangle clip) {
        D3DContext context = getContext();
        context.getVertexBuffer().flush();
        long res = nPresent(context.getContextHandle(), d3dResRecord.getResource());
        context.validate(res);
    }