It's seems to be solved now! I changed the repo directories and tried the update again and this time it did the whole lot without any problems!
It's perhaps a little bit of a time waster really, since the new relase will be out in a couple of weeks, but at least I can get the backups done sensibly now, without having to use the root account to burn disks. Thanks for taking the time to reply too.
Actually, the old 2007 has been very stable and one of the best OS's I've had in a long time, and the updates I've made to now had been selective, since I run apache web server, Mysql and a host of other things on here all the time, using it as my website development pc. The idea of a re-install is daunting, but now I can get everythiong backed up, it's not so bad!