At first, I thought something was wrong as I saw so many more visits than I saw with Google Analytics... After digging deeper though I realised its because so many, like myself, block all 3rd party cookies and trackers so these visits just don't show up. Disqus Comments and Google Analytics are both notorious for deep tracking so it was high time I ditched them.
I've switched to using AwStats which just reads the server logs and displays similar information without the use of trackers or 3rd party cookies. AWStats is a free powerful and featureful tool that generates advanced web, streaming, ftp or mail server statistics, graphically. The site is a lot cleaner now and I must just still disable StatCounter in the coming days. AwStats does what I need for basic info, so I'll be using it going forward.