I have spent way too much time trying to figure out all the quirks of running FishEye / Crucible behind IIS 7 (see for instance here: http://confluence.atlassian.com/display/JIRAKB/OAuth+after+Initial+Configuration+Does+Not+Work). It should be a supported configuration and work seamlessly. There should be a clear step by step guide on what to do on the web server side and how to configure JIRA and FishEye so that they can work together even when using some web front end like IIS or Apache.

I don't think that many people want to run FishEye on port 8060 and start it from command line...