They are not the same. "It's kind of you" is referring to a specific action. "You are so kind" is saying the entire person is a kind person. --------------- "It's kind of you to give me a gift." == Your action is kind. "You are so kind for giving me money." == I think you are a kind person in general.

Really they are about the same, but in the first you are saying whatever they did was kind. In the second, you are making a general comment about the person. Also with the first you would probably add more to the sentence, such as, "It's kind of you to say that" or "It's kind of you to help me".

Joe's answer is correct. The first sentence is a statement referring to a kind act. The second statement is a compliment to the person.