up2date selects packages that have already been previously installed by another method. If any of these packages are selected for update in up2date, up2date fails with a message that the package is already installed.
up2date uses standard RPM database queries to determine the state of your system. It doesn't interfere with manual RPM updates or other rpm-based update systems. Please give a SPECIFIC example of your problem.
the up2date "menu" of packages is built dynamically. It should *not* include packages that you already have installed. I can't duplicate this behaviour here. Please give a specific example. Show the output of rpm -q <packagename> and then verify that running up2date still displays that package as available for download and installation.
user had a corrupted RPM database from a buggy version of RPM. Not an Update Agent problem.