I've not played SC2, but upon searching I came up with this, which I hope helps...
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Under My Documents/Starcraft II in Windows or ~/Library/Application Support/Blizzard/StarCraft II in Mac OSX (not the Starcraft II installation folder), there is a text file called Variables.txt which contains all the basic settings for the game, including graphics and sound options.
In this file, the variables height and width determine respectively the height and width in pixels of your game window on launch. Changing these from (in my case) 1080 and 1920 to 800 and 1024 fixed the problem.
http://gaming.stacke...ide-starcraft-2