So I figured it out and figured I'd leave this here for anyone else that has this problem.
RSyntax Editor causes this problem on the macbook pro with Retina display. You need to either go to a previous release that doesn't use RSyntax Editor or try and use a newer version.
You can turn off RSyntax Editor by going to Plugins and unchecking "syntax" and then clicking unload. Restart and it won't flicker.
Unfortunately this also turns off syntax highlighting.