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Sounds like you haven't separately published the data source to the server. If you publish the data source to the server (Publish a Data Source) then connect to this published data source in desktop, replacing the datasource to use the published version, this problem should go away. Replacing a Data Source | Tableau Software
I have tried this, however after trying to publish my workbook while connected the the published data source (rather than directly to the extract) the option to select a refresh schedule disappears. Is this just a matter of permissions issues and something I'll need to sort out with my Admin?
Once the extract is published to the server you can refresh it at a schedule of your choosing on the server, no need for any manual refreshes. This link will help guide you how to set up the refresh on the server: http://onlinehelp.tableau.com/current/server/en-us/help.htm#schedule_add.htm%3FTocPath%3DAdministrator%2520Guide%7CWork%…
You probably need admin rights on the site on the server to do this.