It happens when i'm trying to position a greenscreen subject into the background. it will not work. i used to have a box that i could move and it disappeared. i'm useing windows 7. Movie edit pro 2014
More than likely you have used the rectangular button in the top right of the effects window that toggles between 'Edit' and 'Preview' modes. MEP remembers your last setting so that if you finished a session with preview active you will have to click on 'Edit' the next time you start the program to get your rectangles back.