When you encode a 16:9 movie (which most are these days), you will end up with a 320 x 180 encode (do the maths) or maybe even less than 180 if the movie is a 1:2.35.
If you change this, people look tall and skinny, etc so I would not recommend it.
This is why you end up with black strips above and below.
Cropping, etc will not help.
PS: Update to the latest Beta.