Export to Excel sometimes loses Jira items. I'm not sure of the exact circumstances but it appears to do it mostly when I have the "Issue Links" column in my export, so it might be related to the size of the "Issue Links" field.

To reproduce, go here http://jira.atlassian.com/secure/IssueNavigator.jspa
and try searching with Project=JIRA and Query="link". For me this returns 969 items at the moment. If I export to excel then I only get 903 issues in the resulting spreadsheet.