If you followed any of the popular hacking guides, or used a packaged script, you probably ran a command that set a flag instructing the TiVo to not install any upgrades. Basically, the upgrade process installs the new software on an alternate boot partition and then switches that partition to be the primary. The program used to set the boot partition and parameters is bootp. This command is run only once, while the drive is being hacked, so it doesn't appear in the init file. Just remember that MRV will be disabled in 6.4a until you rerun superpatch.