I have 2 connectors in the Stash server.xml.
First is the standard connector, but on port "7991". This is intended for the localhost trused applicaiton linking between Jira and Stash. If I also log in using this port I can view the Jira issue popup fine from the commit screen in a Stash repository.
The second connector, on port "7990", has proxyName and proxyPort values. I am proxying through IIS using ARR. Through the proxy when I click an issue I get a "Page not found" dialog box.
If I right click the issue link and open in a new tab the Issue opens correctly in Jira (the link is also through the proxy).
So far everything else in Stash and Jira seems to work through the proxy.