Movies include a frame size, which is the width and height of each frame, in pixels. Frame size doesn't affect playback, but it can affect exporting: it's needed to calculate the scaling factor when you export a movie with the "Scale to fit" option. Typically you're exporting to a smaller format, and you want the original frames scaled down so they fit. If the frame size is incorrect, frames may be cropped unintentionally.
The frame size is set to the window size when you start recording. If you start recording before switching to full-screen or Veejay mode, the frame size will be incorrect.
To correct the frame size, use File/Movie/Resize. The command displays a file dialog, allowing you to browse for the movie. After you press "Open", the Resize Movie dialog is displayed. Enter the correct width and height, and press "OK" to save your change.