They really mean the same thing, although you'd be more likely to use the latter when repeating yourself or to be clearer.

You might say "what I mean is.." if you made a mistake or said something wrong. It is a way of correcting yourself, and sounds more apologetic. People often use "I mean" as a filler word, such as "um..." or "like..." or "ya know..." Especially when talking about something that could be controversial or personal. "I mean, why do people always say these things?" or "I am getting tired of President XXXX, I mean, why does he keep lying to us?"