Thanks.
Both machines were a clean install and then a restore from a v7 backup via server manager. However since then the x64 machine has had another clean install and restore from backup due to hardware failure.
Looking at bash history, on both machines at some point I've run a command that disables the base and updates repos. I've a feeling it was to do with a bug, but I can't remember what exactly it was. The x64 machine's hardware failure was relatively recent so that is probably why all the repos are enabled in it.
Both machines are at different sites and are not connected.