Thank you for the info Charlie, for usually I am able to find something if a rules issue is present; however, I have found no evidence that there are any open known issues regarding the rules for this bulletin.
Further research for NDP20SP2-KB2789643-x86.exe & NDP40-KB2789642-x86.exe; found both are bundled in MS13-015. This bulletin was released on 2/12/13 with no revisions, nor was it superseded, since then. Often this will cause a mock-rules issue if the PMImport is not configured to clean up Revised or Superseded updates.
Moving forward: please proceed with opening a separate case for each update to be reviewed by the Patch Management Support Team for a possible change in the IsApplicable Rule data.
Thank you again,
Joshua