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I downloaded the JRun app server from Macromedia (development edition) and installed it on my test server . It does integrate with IIS, and after some configuration will route jsp pages directly to that app server.
So, I'm not running two web servers, just two app servers. Which does make sense to me. ASP needs to be 'registered' with the web server even though ASP is embedded in IIS. Perl, which is similar to an application server has to be registered, and so do the java dlls for JSP.
But thanks for your concern. this is all taking place on my test server - not the production server.