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Unless the original separation agreement is filed with the court you need either an original copy or a certified copy of the original.
As far as why the judge will not sign it may be just because you didn't comply with the separation agreement or it could be the actual forms you used.
Divorcewriter.com as some of the other websites do not replace the work of an attorney. I realize people try to save money and I can understand that but somethings truly should only be done by a lawyer.
This quote is taken directly from Divorcewriter.com disclaimer: "DivorceWriter's goal is to provide self-help divorce documents. However, DivorceWriter is not a law firm and only lawyers are allowed to issue an opinion regarding the legality of a document and its applicability to your specific circumstances. If you have any doubts as to the applicability of your DivorceWriter purchase to your situation, you may wish to seek the advice of a lawyer licensed to practice law in your jurisdiction.DivorceWriter offers a full refund if your documents are not accepted by the Court."
As you can see they are not lawyer and though some judges may accept less than perfect divorce papers there is no guarantee that all judge will accept such documents.
You have two choice where you can attempt to supply an original separation agreement or just retain an attorney. I suggest you retain an attorney but the choice is yours to make. Call the local attorney bar association to find out if there are local attorneys who are willing to offer services either free (pro bono) or at a reduced rate.