Apparently, when doing "yum update ", and it fails miserably, you can end up with duplicate versions of packages in the RPM database. This seems harmless, but is annoying. yum provides a tool to check for this, but I was not able to find anything that would automatically repair it. So here's a little tip:
$ yum check duplicates | awk '/is a duplicate/ {print $6}' > /tmp/DUPES $ yum remove `cat /tmp/DUPES`
Of course, before you remove the dupes, make sure to examine the tmp file (/tmp/DUPES) and make sure it looks ok.
Update:
There seems to be a command to do this, package-cleanup has an option for it. E.g.
$ package-cleanup --cleandupes
However, testing this command on a second box having the same problem gave bad results, it seems to have uninstalled the "real" packages too.