I have seen similar problems to mine but none exactly the same, and noe of the solutions worked. Here it is:
I have played through the Thieves Guild quest-line, completing "A Chance Arrangement" and "Taking Care of Business" without trouble. Then when I finish talking to Brynjolf about joining, and he is supposed to introduce me to Mercer Frey, he walks off to the cistern, and I don't get the next quest. Every time I talk to him, he says "Hmmm?" and when I follow him into the Cistern everybody attacks me. I haven't been to any of the Ragged Flagon locations previously. This is very frustrating as I am playing as a thief player and my whole intention was to join the Thieves guild right away.