You could try just cleaning one section of registry entries at a time, manually label what each backup pertains to (Missing shared dll's,ActiveX issues, uninstaller issues etc) and narrow it down a bit to find the offending entry, by attempting to update the McAfee after each clean. It's probably just one, or a small handful.
Hi in short many Antivirus and AntiMalware do not "correctly" report their registry entries as belonging to them. This is the stop malware writers from easily disabling your program, but it also stops CCleaner from identifying a reg entry as needed. As Tarq said it's probably just one or two. However Please read my Signature and you'll be doing yourself a big old favor.