Do you have some examples? Most of our *nix patch checks are re-written every time a new patch supersedes them...
A few weeks after I posted my query, the "missing updates" weren't listed any more in the patch report. Our Unix sysadmin said he hadn't run patches, and in any case, had applied the "missing" patches long ago, so I am guessing someone at McAfee noticed the problem and fixed it. Who knows.