Maybe a copy&paste mistake in CLCommandqueue.java:

     /**   
     * Calls {@native clEnqueueCopyBuffer}. 
     */ 
    public CLCommandQueue putCopyBuffer(CLBuffer<?> src, CLBuffer<?> dest, int srcOffset, int destOffset, long bytesToCopy, CLEventList events) { 
        return putCopyBuffer(src, dest, 0, 0, bytesToCopy, null, events); 
                                        ^  ^  should be srcOffset, destOffset 
    }