Strangely, I applied to another school at Penn and I'm waiting for the decision but I just got Penn GSE's information CD yesterday. I don't quite understand as I thought the early admission for financial aid and fellowship consideration was in early Jan. (right?) already. Did you apply for the early admission?
I had a problem with recommendation letters as well but my situation was quite different. One of my providers had to go abroad soon before the deadline so I sent an e-mail to the admission office that I was not sure he would send his letter in time and asked them if I could send an additional recommendation letter and I would take up on their decision. They told me it would NOT deter my application. Maybe you can send 3 letters (if that's the number of letters you're supposed to send) disregard another one you asked and not sure if she's written you a good one. And if the admission office chose your 3 out of 4 there's still a good chance that either an important one OR the one who knows you well will be randomly chosen. Fair?