In short, yes. In an uncontested divorce, after the 90 days are up, you would both have to sign an affidavit of consent (which can only be executed after the 90 days), and only then can the court enter the decree. So even if all the papers are filed, but she does not sign the affidavit, the court can't enter the decree, and can require you to go to mediation
/ court to hear out these issues.
Now as a practical matter, if she has signed the papers already (depending on what's in them) you can ask the court to compel performance of signing the papers, as agreed to under the terms of the agreement. Essentially this is a "contract", and since you have already paid, you have performed yourself, but she has not. The court cannot enter a decree at this point if she does not agree (the whole purpose of the 90 days is to make certain both parties do agree to the terms of the divorce and to give them one last chance...)
That being said, since it no longer sounds like this is going to be a mutual agreement, you should contact an attorney in your area that deals with divorce cases. Go to www.lawyers.com or www.legalmatch.com to find an attorney in your area. You should be able to find one that will give you a free initial consultation and better advise you of your rights, any problems with your case, likelihood of success, how courts are treating cases such as yours in your area, and what you should do next.
Hope that clears things up a bit. If you have any other questions, please let me know. If not, and you have not yet, please select the "accept" button. If you have already clicked "accept", or if you will in the future, please let me know so I can track these for my own reports and customer satisfaction stats. Thank you, and again, good luck to you!