On any patch repair jobs I deploy, the machines that have successfully installed the patch still show as vulnerable. I deployed the patch(es) with a scan and repair setting that includes vulnerabilities and I can see from the inventory of an example machine that it does have current vul scan dates. If you look at the attached screenshot, you'll see it shows the patch was installed (ms08-067 in this example) but it still shows it as vulnerable. This seems to be happening with all repair jobs I have been sending out lately, I'm not sure if this started when we deployed 88sp1 or when I trimmed down my scan and repair settings that is included with my agents (though vulnerabilities scan is included with my agents). Both client and server are 8.8 SP1.
