Hey blitz. Welcome to PCHF!
I'm not familiar with McAfee, so I'm not entirely sure any application-specific problems that would cause this. However, it does sound like you may need a repair installation of McAfee.
Also, the scanner will only quarantine files that it cannot clean. For example, I once had an infected file that couldn't be healed because it was in a ZIP archive and needed to be uncompressed before healing could take place. I'm sure there are other situations that would have the same result.
I've marked your thread as [Open] so a Tech can come in and make a more thorough assessment.
Rodents210