This actually seems to have cleared up.
During the time I was receiving the pop up, I had another browser open with a movie paused in it. In order to try and watch the movie, I had tried to download an update for the browser's movie streaming capability. And it somehow caused that popup. Once I disabled that update, the pop up stopped.
I am glad that I went ahead and did the malwarebytes thing because it seems to have really helped my computer's performance.