When exporting a file at 16:9 (1.77:1) the pixel count will round up to display the nearest whole pixel.
This can cause files encoded to 720x405 display a single extra horizontal black pixels at the top or bottom of your video. You may see 2 different aspect ratios depending on what program you open this file in.
To account for this encode your file to 720x404 and it will display correctly.
720 x 405 file opened via Quicktime X Inspector (shows single aspect ratio):
Same file inspected with VideoSpec (shows two aspect ratios and illustrates issue):