So I've followed the instructions in the knowledge base, I'm able to access Jira from jira.mycompany.com:8086 (8080 was in use), but on attempting to access from lira.mycompany.com, I get a mostly blank page with the login box, but no graphics. It's like it half loaded.
I've done the IIS setup as advised, and added the appropriate proxyport and proxyName setting.