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When two windows are open it only seems to know about one. #24
When you start sublime text 2 from scratch up and it loads the plugins, it seems that when it loads the plugins to the empty sublime text 2 editor and then if you open say a project directory and another sublime text 2 window opens, and then you try and Start Guard it will fail telling you incorrectly that it can't find Guard files, etc because it only knows about the original window for some reason.