As the first step, I believe that you should check:
1. JIRA Fisheye plugin is properly working and is updated?
2. Is there any reverse proxy between the servers? In case of yes, did you properly set the JAVA OPTS for both applications?
In case of furher details, may be you should use the following links as your guide line or raise a ticket at https://support.atlassian.com
* Proxy configuration > http://confluence.atlassian.com/display/STASH/Integrating+Stash+with+Apache+HTTP+Server
* JIRA and plugins compactibility > https://confluence.atlassian.com/display/STASH/JIRA+compatibility
* Linking JIRA and STASH > https://confluence.atlassian.com/display/STASH/JIRA+integration#JIRAintegration-LinkingStashwithJIRA
I ran into a similar issue: https://answers.atlassian.com/questions/124191/stash-commits-not-showing-on-source-tab-in-jira
I worked around my issue by disabling trusted applications for Stash accessing JIRA, and use OAuth instead.
I am still using Trusted Applications for JIRA access Stash
There's a thorough JIRA-Stash integration troubleshooting guide available here: https://confluence.atlassian.com/display/STASHKB/Troubleshooting+JIRA+Integration
Hope this helps!
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