I ended up updating Windows and had to re-download Atom, however, I had all my settings brought over with sync-settings. All has been good except something is up with the handling of my files when I click on them in the tree view.
What used to happen was if I clicked on a file, it would open directly to it in my main window pane. Now, however, when I click on a file, it opens it up in a new tab but doesn't switch to it. I have to manually do that.
I've searched everywhere but can't seem to find a solution. Why is it handling my files this way and how can I get it to go back to the way it was?
EDIT: MY SOLUTION
Ends up my issue was the Atom Debug UI package that was causing this behaviour. Once I disabled it, everything went back to normal.