But that aside, heres the most accurate description of what is going on with the error #51 message. When your tivo first boots any hard disk that is in a virgin state (e.g. the tivo OS is loaded to the hard disk but it has never been booted before) what it does is generate a hash key that is seeded based on the serial number of your tivo and some random number, then it stores this information into the MFS database as a value labeled "DiskConfiguration" effectively marking that hard disk to be used in that *specific* tivo.
This key is used as part of the encrypt/decrypt process of your tivo whenever it records any video, and it effectively ties those video streams to your tivos mediaswitch asic so that theoretically you can't arbitrarily give your friends a copy of your recordings (note I say theoretically because we have long since defeated this measure.)
Now, when you take this hard drive and move it to a tivo with a different serial number (and thus presumably a different mediaswitch asic with different private keys,) the tivo will boot up and read the diskconfiguration key, and it will notice that the serial number seeded into that key doesn't match the serial number of the current tivo. Thus it bombs out and assumes that all of the videos currently stored on that hard disk wont be able to decrypt properly, thus it wont allow you to play any streams, and it also assumes that if it tries to record anything new, something else will go wrong as well.
Now that may or may not be the case, dependent on whether or not you recorded those shows unencrypted. Either way though it will turn your tivo into a doorstop, giving you that error #51 message until the situation is resolved. This is where 51killer.tcl comes in. What it does is simply erase the DiskConfiguration key from the MFS database. Thats it. It is really a very simple script. When you reboot your tivo, it'll notice that the diskconfiguration key is not there, so it will assume that the disk is in a virgin state (even though technically it isn't,) and it will then generate a new diskconfiguration key and then tie the hard disk to its current serial number, and all new CSO keys for the new recordings will be generated (or not, if you hacked tivoapp properly) based on that new key.
Note also that clear and delete everything does pretty much the same thing. C&DE clears out every value and every object that is not essential for the tivo to actually function - to include the diskconfiguration key. Thus when it reboots, you have the same effect, just like plainbill said. The whole purpose of 51killer.tcl is to be able to remove the error #51 message without being destructive to all of your recordings, settings, season passes, etc as opposed to what the C&DE does.
Now in your case, one of two things is going wrong here. Either you didn't actually do the C&DE (you probably selected the wrong option, it is the very bottom option that is specifically labeled "Clear and Delete Everything," as in it totally nukes all recordings, thumbs, season passes, etc.) or there is something wrong with your crypto chip (although this is quite doubtful.)