Problem description:
JIRA links in old Confluence instances can be missing their serverID-parameter.

Steps how to reproduce the problem:
1. Running any version of Confluence between >= 5.1 and < 5.4 (tested with JIRA macro plugin up to 5.3.4).
2. Create an application link to a JIRA server (was tested running JIRA server 6.1.9 but I believe this to be independent from the actual JIRA server).
3. Copy a JIRA link to an issue and paste it into a new document in Confluence.
4. Save the document.
5. Check out the documents storage format.
6. Note that looking at the storage format, the severID-parameter is missing.
7. Upgrade Confluence to >= 5.4 (tested when upgrading to 5.4.3, but I assume the issue persists even when upgrading to the latest Confluence version including 5.8.13)
8. Check out the storage format of the test page.

Actual result:
The storage format does not specify the serverID for that issue to the JIRA server.

Expected result:
The storage format shows the proper serverID.

The problem is here as follows (at least all according to my assumptions/observations):
In Confluence 5.1-5.3.4 there was a bug resulting in the serverID not being added when copy-pasting links directly from Confluence.
There is actually an upgrade task ("jiraIssueMacroServerParamsUpgradeTask") which correctly adds the missing serverID. However, this upgrade task is only run when upgrading from Confluence <= 5.0.x.
Due to the bug in Confluence 5.1-5.3.5 upgraded Confluence instances can however still contain JIRA issues which are missing the serverID.

Therefore I'd suggest to perform the jiraIssueMacroServerParamsUpgradeTask as part of one of Confluence upgrade tasks for one a following version (Confluence 5.9 or 5.10 for instance). That way any older remains of this old bug are fixed correctly and won't cause problems in the future.

The issue is related to CONF-25329 and the support request I had a while ago (CSP-146293).

Workaround

1. upgrade your instance to Confluence >= 5.4
2. go to admin/do-force-upgrade.action
3. manually run "jiraIssueMacroServerParamsUpgradeTask"