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Creating S-parameter files uses ADMS, so you need to follow all the rules of SPICE. Make sure that the value of your TEMP or TMP environment variables do NOT include any space characters. If you don't define these explicitly, Windows uses a default folder under "Documents and Settings" so there are spaces in the folder name. I suggest explicitely defining HOME and TEMP to something simple, without spaces, like HOME = C:\home\myName and TEMP = C:\home\myName\temp.
If that doesn't fix the problem, try running a transient simulation of your net forcing HyperLynx to run the simulation in ADMS. That might give you some more clues about what is going awry.
I thought I would post this. The path where the software is installed must not have any spaces in it.