Yuck - I NEVER install DB servers, Apache or PHP from a distro's install screens. Your best bet might be to just download the latest source tarballs / bzballs for the packages, and then configure and make / install them. They SHOULD overwrite your old installations, but that is not guaranteed since you apparently used RPM? Stay -away- from RPM - it is only trouble.
What I WOULD have done (had I not used RPM) and I was you was to just go and stop all the services running off the old installations (apachectl stop, killall mysql, etc) I would then physically delete all the installations' directories (I would know where they are, since I did not use RPM, but a source install...) and then simply install the new packages.
The reason why you are probably getting old version numbers even after a new install is that RPM probably put them somewhere non-default... which a tarball's source usually does only on specific option.