Steps to reproduce:

1. install JIRA 6.1 and Stash 2.8.1
2. set the Base URL to using direct URL (eg: http://localhost:8080/jira and http://localhost:7990/stash) instead of the FQDN
3. create the Application Link using the direct URL
4. edit the Base URL to use the FQDN (eg: http://example.com/jira and http://example.com/stash)
5. In the Application Link, edit the Display URL to use the FQDN
6. create sample issue in JIRA and try the "Create Branch" link. It will re-direct the user to http://localhost:7990/stash instead of http://example.com/stash
   the expected result is to get the user to be re-directed to the http://example.com/stash when user click on the "Click Branch"

On a side note, different behaviour is observed for JIRA 6.1 and FeCru 3.1.4:

1. install JIRA 6.1 and FeCru 3.1.4
2. create the Application Link to use direct URL instead of FQDN
3. edit the Display URL to use the FQDN URL
4. create issue and try to Create Review from the Source tab
5. user will be re-direct to the FQDN URL of FishEye