After upgrading an alfresco container from ubuntu 8.10 to ubuntu 9.04, the web client worked fine, but the files didn't show up in samba, and the ftp just had the Alfresco and AVM folders with nothing in them. The problem is that during the upgrade, samba was installed, which overrode alfresco's samba. The problem was fixed by stopping and disabling samba, then restarting alfresco.