What have you tried so far?
Have you shut down and restarted StrokeIt?
Have you tried running it in Admin mode (in Windows 7, right-click the shortcut or .exe for StrokeIt and select "run as admin".
Have you checked the settings in StrokeIt's preferences/settings? Make sure the right activation key is selected (right mouse button, or whichever you use). Look through your list of applications and check whether the checkbox "disable for this application" is unchecked for the application "Global Gestures". If it is checked, no gestures will work, except in those programs for which you have specifically set them up.
Good luck!