We are saving config on a central management server. On the router we configure tftp-server system:running-config and tftp-server nvram:startup-config.
We never had problems until we start a VPN service with IOS 12.2T and 12.3 3DES releases. "tftp-server nvram:startup-config" gives proper results. "tftp-server nvram:startup-config" gives files with no content.