I've never heard it either, but my first take was that it was a play on that "Got milk?" advertising campaign. In that case, the response would be "Got milk!" So perhaps the "Got flattered!" was a response to just getting a compliment. However, I suspect that would be more an American usage. Don't know if that milk ad runs anywhere else. My two cents anyway.
Not negative. Actually it's a way to be nice to the other person, like, 'your opinions count for a lot, that's why I am flattered by your attention.'
But it surely is negative when a woman uses 'Im flattered, but…' to turn away a suitor, as a way to be gentle. But that is too close to home here.