I also run MSE and am now worried that it is no longer regarded as being anywhere close to adequate. Even Microsoft have admitted this, so I'm told.
So I have 2 suggestions. Add Spybot S&D and run a scan, that picked up a Trojan that Malwarebytes had missed on my PC.
It is probably, also, worth running McAfee's Stinger, although, in recommending this I am above my pay-grade.
Then you may have to consider replacing MSE with another of the Free AVs. I am not competent to make a recommendation there.