Some folks might suggest hiding the offending updates, if you are sure they are already installed, but I feel that might lead to problems later. Maybe hide them for a few days only for testing. When you tried manually installing the updates, you did so while in Safe Mode?
Have you tried uninstalling the updates and letting Windows reinstall them? Open Windows Update and use the "Installed Updates" option on the bottom left. If the updates are listed there, you should be able to uninstall them.
The last thing is to rename or delete the SoftwareDistribution folder in the Windows Directory. If you do this, it will rebuild the data base, but will take some time to catch up.
But basically, the system has gotten out of sync as far as these updates and needs to be reset somehow. If the updates were to show failed on the Update history, you may be able to right click and get a reason.