MacBook Pro :: Display Shrinks When Running Application Modified By SwitchResX

I play the Elder Scrolls Online and was trying to tweak around with the game's settings to get the most frames possbile while running the game with a high level of rendering samples. I did this by lowering the game's window resolution by one level while in full screen. However, after a recent update the game's true full screen no longer works and I'm unable to change the game's in-game resolution. The game automatically sets itself to my Macbook Pro's native display, and this results in a frame rate drop. 

As a workaround, at least until it was fixed, I would lower my Macbook's native display before running the game, and restore it when I was finished playing. This was tedious to me, and I looked around for a program that would automatically change the display on a specfic application's startup or exit. I found SwitchResX at [URL] and wanted to try it. I made it so that the resolution would switch to 1280 x 800 whenever ESO was loaded. It worked fine, but I wanted to do a comparision of frames at the normal resolution to see if it actually fixed anything. This is where my problem lies: after closing ESO and disabling the SwitchResX setting, the entire screen shrinks down to a small square whenever I run other applications (initially I thought it was just with ESO, but I found out that more programs were affected while typing this), and most of it is surrounded by a big black border: 

(You can see the tool bar and the application dock hanging in the middle of the screen)

I've tried:

Uninstalling SwitchResX

Changing the display

Changing the display while running the programs affected

Soft Reseting

Hard Rereseting

A NVRAM Reset

Info:
MacBook Pro with Retina display, OS X Mountain Lion (10.8.4)