Please note: this issue is marked as resolved in Confluence 5.5, but you will also need version 6.2 or later of JIRA (and if using JIRA Agile, 6.3.8 or later)

In the meantime, it's possible to manually force the cached count to be updated by making an edit to the Confluence page.

With JIRA 6.1.5

Steps to Replicate

1. Ensure the Application Links is configured correctly
2. Ensure Remote API Calls is enabled in JIRA
3. Create a new space with a new page (e.g: 'Page A') in Confluence, and insert a new issue using JIRA Issue Macro in the page
4. The JIRA links button is displayed in this new page
5. In JIRA, try to link an Agile Report/Board/Sprint to the newly created page ('Page A')
6. Go back to Confluence, click on the JIRA links button in the 'Page A' and see if the JIRA Agile Report/Board/Sprint is shown
7. Create another Agile Report/Board/Sprint and Link it to 'Page A' in Confluence
8. The link is missing

Scenario 2:

1. Make a page A in Confluence.
2. Link to that page from JIRA.
3. No links are shows on page A in Confluence