Hi there,
I can't really help you with your worries and it seems that a lot of people experience problems with unreliable recommenders. A similar thing happened to me:
<<skip this part if you don't want to read my story about late LORs>>
I asked all the professors months before the deadlines (mid-September), met most of them in person, provided them with all the information on time, sent out the invitations on time, sent reminders and did all this while remaining absolutely polite and understanding. Still, I am missing one recommendation letter for one program that closed the appl. process on Dec 8th. I repeatedly asked this one professor (politely!) to submit his letters but I only received one of two, with the former being submitted one week late and the latter perhaps not being submitted at all. I wrote to the school and asked what the grace period is and they answered that they would start reviewing during the winter break. I called the professor, wrote to him again, tried to meet him at the office (impossible, because winter break has already started at my school) and, out of sheer despair, even contacted one of his colleagues. This helped, he submitted this one late letter, but not the second one.
I remember that, when we were discussing this issue in his office, he mentioned that he recommended somebody before and was rather confused by the online recommendation process. This should have raised some flags. At this point however, I did not think too much about it, because I thought, clicking on a link and hitting a button should not cause too many problems for a university professor. Naturally, this is very disappointing for me. If I were rejected from the school, I would have liked it to be my fault (i.e. simply not being competitive enough) but not because my application is not reviewed due to being incomplete. I could also be mad because the time and money (it is the most expensive program, 125$) on this application was apparently wasted, but I am mostly said because I really would have liked to have a chance. I don't feel that I could have done anything more. Even worse, I planned fo this professor to be the recommender for two other programs where the deadlines are mid-January. I should probably try to exchange him for another recommender, which is close to impossible on this short notice and at this time of the year.
<<end of story>>
Although this does not help me anymore, in response to LindLLL, I'd advise you (and all the other people in this stressful situation) to do this:
If you still haven't received the letter, write to the program and explain your situation. Ask when they will start reviewing the application, they might give you the ultimative deadline for the recommenders or at least an approximate period of time when it is still okay to send in letters. With this info in mind, try to get in touch with your recommender. If possible, do so by phone or in person, especially if she is rather unreliable and unresponsive. Do not give her the real deadline, but one or two days less, to make sure that the letters will be submitted for the definite deadline. If you get the chance to talk to her, ask her if you can do anything to help her with this (provide more information, prepare a sample letter or even come to her office when she clicks through the recommendation form so that you can assist if she does not know what to do).
I'm not sure whether a replacement is a good idea. Firstly, generic and weak LORs can hurt your application. On the other hand, two stellar and one mediocre LOR in combination with a strong application package (GPA, test results, SOP a.s.o.) is probably better than having your application rejected because of a missing LOR.
I hope everything will turn out well for you!