What is the source video you are using? Do you know the aspect ratio on the source file and are your settings trying to change the aspect ratio?
There is also a correct term for when those black pillar borders are added to video I cannot remember exactly what that is called but they may be added to any video by choice while encoding. Because of that youtube recommends not adding them so that their player will correctly display the video. This could be where you are running into problems. If the option is set as default it will add those bars.
What software are you using or I should ask what all software have you tried converting with so far?