When you configured the tomcat connector $JIRAinstall/conf/server.xml file, did you only set the connector to use this new proxy connection? I ask because I would be interested to learn more about trying to bypass that proxy. One way to do this would be to have two different connectors for Jira: one for the proxy, and another connector on a different port that can in turn bypass that.
I understand that the point here is to get it working with IIS, but just having this other connector can be helpful to troubleshoot and understand exactly where the problem might be. I suspect this could be a setting in IIS in regards to rerouting requests, but it's difficult to tell so far with the information we have.
Also, are these other applications on the same server as Jira? Where do these applications exist in relation to both Jira and IIS from a network standpoint? I am curious to learn if perhaps there is a way to have these applications communicate with each other without having to go through the proxy at all. That might not be possible, but it might one way to get around the current problem.
Also which other applications are you trying to login to via Jira? I am interested to see what sort of error messages might be presented in the logs of those applications like Confluence, it could be this might offer us a clue as to the nature of this particular error.
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