If you like the Project Timeline view like most folks do then you probably use the one in the Project Site as well. Depending on your setup, however, you may notice that the timeline in your Project Site does not reflect the same reality as the timeline in Project Web App. Well actually the information in the timeline located in your Project Site is kept up-to-date via the task list in the Project Site. Therefore if your task list information is not being synchronized the timeline will be off. To check this edit your EPT and locate the Synchronization settings. Once in there be sure to select the checkbox for Sync SharePoint Tasks Lists. Once selected the task list will be synchronized upon project published and your timeline should reflect reality!
