problem of synaptic

[bastidesamuel at neuf.fr]

I wanted to install a samba server rpm (build by me ) but i had a samba
client there is an incompatibility ,So I wanted to uninstall samba and
reinstall this with synaptic
 i have check that it doesn't work for me when i have lauched synaptic ,
it said to me that

" There are multiple versions of "gpg-pubkey" in your system.

This package won't be cleanly updated, unless you leave
only one version. To leave multiple versions installed,
you may remove that warning by setting the following
option in your configuration file:

RPM::Allow-Duplicated { "^gpg-pubkey$"; };"

There isn't probably any concordance but it happen now and i don't know
where is the configuration file of synaptic or apt


More of that it seems after that all of package of Nautilus and KDE have
been uninstalled and i wanted to go in mines files graphically so i have
reinstalled these with "package manager", no problem they have been
reinstalled 
but I don't know why they have been removed ?
So after up2date cannot update them (multiples rpm)...
Only a reinstallation of fedora can clean that ?