If it continues with "So what you're saying is ..." that means the speaker is going to totally misunderstand your last statement, and supposdely repeat it back to you using other words, when in fact it will be the opposite of what you have just said.
Similarly, just saying "So ..." is a shortened version of the above - cutting straight to the misnunderstanding.
It's the hallmark of people who don't listen, or having listened, have failed to assimilate the information they have just heard becuase they are waiting to disagree.