problems with reinstallation of deb packages from repositories

Hi, It is just me, or have people noticed problems while creating debs from freeradius.org and upgrading them from (local) repositories? Whilst upgrading with debs from command line (dpkg -i), normally works ok, installing them with apt/aptitude install normally breaks the configuration to a point I have to recover /etc/freeradius from backups to be back on track. I have noticed this since setting up a local apt/deb repository. Has anyone noticed this? Regards, Rui