MSE is alright. Its alot better than it once was I'll tell yah that much. Personally I use Avira but it does have some minor popups in the bottom corner. It doesn't do it while you're doing things, just when you've been idle for a while. Wouldn't recommend it to everyone for that reason though. You can pay to get rid of the popups but I'm a cheap bastard.
@OP Hmm, I'm kind of running out of ideas. Since things are refusing to install maybe the supposed virus turned off one of the essential services? Start>run> type services.msc > enter > sort by startup type, screen shot the disabled ones, sort by status, screenshot disabled > upload to imgur please.