Well, this probably has nothing to do with your situation, but... I updated my IntelliMouse driver, and then found StrokeIt stopped working. The reason was (1) I have it set to use the middle button, and (2) the IntelliMouse installation had given my middle button a new default action. Changing that setting made StrokeIt start working again.
So check to see if any other app is looking for events from whichever button you're using for StrokeIt; and try changing the button StrokeIt uses and see if that make it work.