hi,andy_dev_in.
i encounter a similar situation like your's before though i was not using URL rewriting. i wanted the .pdf file to be processing by asp.net rather than by IIS directly, when using VS 2005 web server, i didn't have to add a application mapping in the web server (i also don't know how to set the VS 2005's built-in web server, i can't find a place to set), the pdf file is processed by asp.net successfully. it seeems ( i am not sure) that the built-in web server has a "built-in" application mapping for pdf file.
but in iis, there is no such built-in application mapping for pdf as welll as .Shirts files and .Category files, so you have to add it yourself. You can add it in IIS, in Home Diectory or virtual Directory\configuration
What really matters most is the chance to communicate with you, my friends, rather than marking my post as answer, though I would be really appreciated if you do so.