After comparing my code to the examples and some experimentation I have found that this is being caused by myfaces1.1.3, switching to 1.1.1 and the problem goes away.
Set org.jboss.seam.core.init.myFacesLifecycleBug=false for 1.1.3
I am having a problem when there is an unhandled application exception. After this exception I connot navagate anywhere in the app without receiving another exception "No active conversation". I can't seem to find a way to recover. I have found I can run the page debug.seam and things start working again. Also it depends when the exception occurs it seems to be a problem only during the render phase or when receiving the Facelets formatted error message.