some more details to this ongoing issue
you really should NOT be booting in "init5" AS root
a lot of distros have already BLOCKED ( disabled )this from being done .
( red hat and Debian still allow it )
it asks me for the root password,
if using Gnome as root ,there can be a normal problem CAUSED by logging into gnome AS root when "pam" dose not recognize root in the gui
programs will still
ask for the root password but with you already root in the gui ,it will error if root logging into the GUI is blocked .
But this should NOT be the case with you
run Gnome as a normal user
and use the terminal to become root
" su" or " su - "
now the top panel missing ( past posts ) is NOT normal
add that to gnome not recognizing root
being root and having the yum gui ASK for the root password
is a normal problem caused by using " the 'pam' hack"
to allow root logging into the gui , but you did NOT use that so that is not the cause .
so something " very bad" happened if root is not root any longer
a possible cause
but NOT a fix
rhel5 ( and therefor oracle 5 ) is VERY incompatible with A LOT ( most ) third party repos
most WILL want to overwrite critical system files with different rpm's
5 IS VERY susceptible to this
the yum plugin " yum-prioritizes" ( or on a server "protect-base " is better)is needed to stop this from happening ( unless you DO want it to .sometimes this IS wanted )
can you post the output of this
as a normal user run
yum repolist all
it is looking like incompatible rpm's are installed
A question where exactly did you get the 3 updates and 2 new packages to install ?