The file you are talking about and the one that is binary is called strokes.bin and it's in Gestures folder. If that gets corrupted then much more aggressive errors would result e.g. the program crashes. The files MKairys asked you to take a look at are plain text config files with extension .cfg and they are located in the Actions folder.
If there aren't any entries in any files having "gesture = \ Down" then it is possible, that you taught StrokeIt to identify "\Down" as another gesture which is linked to closing active window by one of your config files (possibly default.cfg). "\Down" does not do that by default as far as I know and it is definitely not hard-coded to do that.