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This is because JIRA is limiting the number of records back to 1000. Unfortunately the JIRA API does not allow you to specify the start page so we cannot query in batches (which we do with Bugzilla for example). So the solution for now is to enter a date limit in the Custom 05 field of the JIRA Data Sync configuration.
I.e. go to Administration > Data Synchronization and click on the JiraDataSync "Edit" hyperlink. Then in the Custom 05 box, enter:
and that will limit the issues to those added since May 2012 or later.