I have experienced the same issue. Does anyone have a solution?
In my case, it is a Project 2007 file using Project 2010 as the application. If I unshare (in order to synch a different project) and then share again, it seems to not recognize that the project tasks in SharePoint are the same ones in Project (where they originated). Similarly, if another person opens the same Project file and tries to share to the same SharePoint project task list, it doesn't only duplicate the tasks, but it duplicates the entire hierarchy (summary tasks and tasks).