I have been having this problem for some time. If I create a new movie and set the video width and height to 640x280, the preview is smaller than 640x280. After I import all of my assets, create my movie, and then export to .flv, the final movie captures a wider area than I previewed.
My work around for this has been to make sure the movies or images I use are expanded about 10% outside the bounding area of the preview area. It takes awhile to get this right and can be frustrating since it is not an exact science.
If you have experienced this problem and understand what I am doing wrong, please help me. I am online and available almost around the clock.