Just for convenience: if you establish an application link between JIRA and Confluence and use an explicit port declaration (e.g. https://wiki.blah.tld:443 instead of https://wiki.blah.tld) the linking of JIRA issues to wiki pages fail.
If you mention a JIRA issue inside your Confluence, the JIRA issue itself contains only the information: "You have no permission to view this wiki page". Manual search of wiki entries inside an issue is not possible. You will receive no warning or errors, just an empty result set.

confluence/logs/catalina.out contains the following line:

2012-12-23 14:17:35,202 WARN [http-8082-4] [auth.trustedapps.filter.TrustedApplicationFilterAuthenticator] authenticate Failed to login trusted application: jira:6281431 due to bad URL signature.

This issue was already mentioned in BAM-11309 and https://ecosystem.atlassian.net/browse/TRUST-31 but is a generic problem with application linking.

Resolution: Remove the port from the application link URL.

I filled this issue to help any other users having the same problem and searching only for JIRA/Confluence.