When the link is established, fisheye takes the physical hostname of the machine fisheye is running on. It will never respect a valid alias in DNS or whatever you type in the URL. I consider this as a defect or at least a strong point to improve.
We temporarily changed the hostname, established the link and renamed the host again. Now Jira shows the hostalias we want it to have.
In the application link screen, JIRA should display you a message saying something like:
"The application link couldn't be reached. Click here to reallocate"
Clicking on the link will allow you to modify the application link URL.
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