I emailed the admissions people and got this reply: "Thank you for your interest in Cornell University. In reviewing applications, Cornell admissions selection committees use your highest sub scores for the SAT/ACT and SAT Subject Tests, regardless of how many times you have taken the exam or whether your highest scores come from SAT/ACT exams completed on different dates. Cornell does not participate in score choice-we require all scores be sent to us. We will create the best possible scenario out of your individual scores for consideration for admission."
Also this site lists cornell as superscoring the "act and sat" so I'm assuming that they do take your best subscores. http://prepmatters.com/sites/default...%209-29-11.pdf