This is a well known issue but it seems that a lot of people are re-discovering it as the 7.1/7.1a comes down the pipe. So we will review the basics:

1. Blocking software updates on a SA unit (by modifying rc.sysinit, setting $upgradesoftware to false, or any other means) WILL cause issues. This happens because the mothership and the box are "out of sync" with regard to the software version they expect to be running on the system. This is generally not an issue on DTiVo boxes, since they do not need to interact with the mothership.

2. Running a version of the software that the mothership does not expect you to be running will often cause you to receive keys that do not operate correctly on your current software version. This happens because (for various reasons) the mothership sends keys based on the software version it expects you to be running, not the version that your box reports during the call. So, if you are on the 7.1 list, but still running 4.0.1b, you will receive keys for 7.1 that do not necessarily work on 4.0.1b. Daily calls also wipe out unauthorized keys in /State/Keyring, so if you are running set_mrv_name.tcl on a subscribed SA, your MRV key will disappear. You will also see nightly reboots as the machine attempts to install the new software. Patches for several versions that attempt to work around these issues can be found here.

3. Running the wrong software version will sometimes cause the mothership to refuse to send you guide data. This may happen a few weeks or months after you have been selected for the software update. If this happens, the easiest course of action is to take the update. There are other ways around this, which you may want to explore on your own.

4. If you are using a "TivoScripts" / "Sleeper ISO" partition setup, taking the upgrade will usually make the system unbootable. You should remove the TivoScripts setup at your earliest convenience to prevent this and other serious problems caused by this program. Read: 1 2

For more general information on software updates: link