Brand New MacBook Pro Retina Glitches
Did you migrate an account from an old machine? It doesn't look like a hardware problem, but it could be corrupt preferences. Bad video cards will corrupt the whole screen, not have it confined to a single window like your screen shot shows.

Try moving the preferences for Messages.app from your ~/Library/Preferences folder to the desktop. You will have to re-configure messages, but you can always put your old prefs file back.  If that works then you probably have a corrupt Messages prefs file. Try that for each app to see if it helps.