That's odd that the scheduled extract refresh is not completing but also not showing an error message. It's doubly strange that the Run Now works flawlessly - there's no prompts or requests when running? Have you checked out the "Background Tasks for Extracts" administrative view? Background Tasks for Extracts It may provide some insight into what's going on and why it isn't completing.
Another possible idea, do you know the exact time the extract should have been scheduled to refresh? The Backgrounder logs may provide some insight into the issue by taking a look at what was going on with the backgrounder during the time it was supposed to execute the refresh. Server Log File Locations
If both of those tools do not assist in resolving the issue, might be time for a case with Tableau Technical Support: http://www.tableau.com/support/request
Thanks and hope that helps!
Honestly I forgot about this post!
We still aren't sure why it wasn't queuing under tasks but since then we've changed our setup from one backgrounder to four which has solved a lot of performance issues and "resolved" this issue too....
Thankyou for your comments