I am always puzzled by the use of the expression "I am flattered". To flatter someone is, in most cases, to praise her insincerely and excessively for gain or advantage; sometimes the praise can be both sincere and true, but the motivation for gain or advantage is still there, which is why flattering is still not a decent thing to do in such cases. Accordingly, if we say of a person A that she flattered another person B, we are giving a negative evaluation of A.
Suppose I was B and A praised me. Now if I responded to A by saying "I am flattered", I would not be giving a negative evaluation of A. But why? Isn't it the same fact that was being expressed when I said "I am flattered" and when a third person said "A flattered B"?
One possible explanation is that when a person says "I am flattered", she is trying to be modest, that is, what she means is "You are praising me too much". This is not, however, a completely satisfying explanation, for "praising someone too much" does not seem to mean the same as "flattering someone".