There doesn't seem to be any functional impact, but these exceptions are logged at JBDS startup - and when a query is run:

!ENTRY com.atlassian.connector.eclipse.monitor.core 4 0 2014-04-04 11:55:23.502
!MESSAGE Monitor failed to start
!STACK 0
java.lang.NoClassDefFoundError: org/jdom/JDOMException
at com.atlassian.connector.eclipse.monitor.core.InteractionEventLogger.<init>(InteractionEventLogger.java:48)
at com.atlassian.connector.eclipse.monitor.core.MonitorCorePlugin.getInteractionLogger(MonitorCorePlugin.java:184)
at com.atlassian.connector.eclipse.core.monitoring.Monitoring.logJob(Monitoring.java:54)
at com.atlassian.connector.eclipse.internal.jira.core.service.JiraClient.getAvailableActions(JiraClient.java:422)
at com.atlassian.connector.eclipse.internal.jira.core.JiraTaskDataHandler.addOperations(JiraTaskDataHandler.java:1085)
at com.atlassian.connector.eclipse.internal.jira.core.JiraTaskDataHandler.createTaskData(JiraTaskDataHandler.java:204)
at com.atlassian.connector.eclipse.internal.jira.core.JiraTaskDataHandler.createTaskData(JiraTaskDataHandler.java:195)
at com.atlassian.connector.eclipse.internal.jira.core.JiraTaskDataHandler.getTaskData(JiraTaskDataHandler.java:162)
at com.atlassian.connector.eclipse.internal.jira.core.JiraRepositoryConnector.getTaskData(JiraRepositoryConnector.java:504)
at org.eclipse.mylyn.internal.tasks.core.sync.SynchronizeTasksJob.synchronizeTask(SynchronizeTasksJob.java:260)
at org.eclipse.mylyn.internal.tasks.core.sync.SynchronizeTasksJob.synchronizedTaskRelations(SynchronizeTasksJob.java:170)
at org.eclipse.mylyn.internal.tasks.core.sync.SynchronizeTasksJob.run(SynchronizeTasksJob.java:154)
at org.eclipse.mylyn.internal.tasks.core.sync.SynchronizeTasksJob.run(SynchronizeTasksJob.java:135)
at org.eclipse.mylyn.internal.tasks.core.sync.SynchronizeQueriesJob.run(SynchronizeQueriesJob.java:225)
at org.eclipse.core.internal.jobs.Worker.run(Worker.java:53)
Caused by: java.lang.ClassNotFoundException: org.jdom.JDOMException cannot be found by osgi.identity; osgi.identity="com.thoughtworks.xs
tream"; type="osgi.bundle"; version:Version="1.3.0.v20100826-1640"
at org.eclipse.osgi.internal.loader.BundleLoader.findClassInternal(BundleLoader.java:416)
at org.eclipse.osgi.internal.loader.BundleLoader.findClass(BundleLoader.java:336)
at org.eclipse.osgi.internal.loader.BundleLoader.findClass(BundleLoader.java:328)
at org.eclipse.osgi.internal.loader.ModuleClassLoader.loadClass(ModuleClassLoader.java:160)
at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
... 15 more