I have had this issue too after upgrading from 9.0 to 9.3. Some of my extracts and live connections associated with workbooks were not refreshing on the Server. The "test connection" feature was inconsistently failing. Republishing the workbook didn't not correct it. Our workbooks contained both a published data source and an extract that was associated just with the workbook.
The only fix, which we discovered through trial and error, is republishing the workbook after following these two steps locally:
Step 1: Go to the data source pane and click "Update Now" for the data source. That will pull data into your workbook.
Step 2: For that data source, on the main menu, do the following: Data-->Data source name-->Refresh