This issue was originally raised against Confluence (http://jira.atlassian.com/browse/CONF-17549). Since then we have created a patched Felix 2.0.1 version which will be included in Confluence 3.1 and fix the issue if Confluence starts first.
To also make it work reliably if JIRA starts first we patched and upgraded the Felix 1.2.1 version of Plugins 2.3.x (https://studio.atlassian.com/browse/PLUG-493). To fix this issue you either need to upgrade JIRA to use Felix 1.2.1-atlassian-9 or create a new release of Plugins 2.3.x and included that in JIRA.