Well
Kev asked if gcc 4 was on bob, and it wasn't, so I spent some time looking around. I think I managed to install something that is not on the RHEL3 up2date server, and that fixed a dependency for a php update unintentionally. This caused the php update to happen, which started a chain of events that nearly resulted in a complete re-install of bob. Ant saved me, having and on there meant I could download a new krb5-libs package, which meant ssh, scp, wget, ftp, lynx and up2date started working again, up untill that point I thought we had lost the fight.
Long story short, after fighting with it for a very long time, I *think* everything is back up and running.
And just so I remember, the php configure settings were './configure' '--with-apxs2=/usr/sbin/apxs' '--with-pgsql=' '--with-mysql' '--with-zlib' 