Can you send the full output of the up2date command (if you're using the GUI, open up a terminal and run "up2date-nox --update" or similar) as well as the outpout of the command "rpm --qf="%{N}-%{V}-%{R}-%{ARCH}\n" -qa" ? That will help diagnose the problem.
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David Aquilina
david at starkindler.us