If you are refering to the Windows "out of date" warning, it does not. If you are refering to a virus or spyware you'll need to be more specific; are these just popping up on their own or are they normal popups from visiting webpages? McAfee VSE 8.8 includes the spyware module as part of VSE 8.8 but not as a part of VSE 8.7 does not, so if it's spyware 8.7 patch 4 may or may not catch it.
If you are licensed to do so, I would recommend going to McAfee VSE 8.8.
This happens when the user is visiting a Webpage. It is the Fake Alert. Also tells them that Virus software has expirered.
Doesn't popup on its own.
McAfee Virusscan does not yet have popup blocking software, generally popup blocking is handled by the user's browser. Not sure if McAfee has any enterprise software that does pop-up blocking. Internet Explorer has pop-up blocking built in, and if you're are using another browser like Chrome or Firefox you can install the free Ad-Block Plus which can block many pop-ups without further configuration. Unfortuanly there's no centeral management of Ad-Block Plus so it probably won't be a good fit if you have more than just a couple users.
If you are running a firewall that can block URLs you could find out the URL of the pop-up ads and block them at the firewall.