Well I guess that I am different then most people. I would have replied with "was that a compliment?". When social skills are lacking, it usually is because no one taught them the correct social skills. Don't sound sarcastic when you say it, sound earnest when you reply "was that a compliment". Most people are unaware that their attempt at being nice is comming across negative. Pointing it out might prevent them from doing it again to someone else.