Why does handBrake rotate my original videos?
Why:
Some programs like quick time, automatic rotate the video when they display, but the original file is still not ok. Please try to see your videos using vlc or other apps. handBrake only rotate your videos if you set that option.

How:
You can rotate the video if you fill the Additional options in the bottom. If you like to rotate 90 clockwise with "Custom --rotate=4" or 90 counter-clockwise with "Custom --rotate=7".

the full parameter list is:


1 : x flip 
2 : y flip 
3 : 180 degrees rotate (also the DEFAULT) 
4 :90 degrees rotate (clockwise) 
5 : 90 degrees rotate + y flip 
6 : 270 degrees rotate + y flip 
7 : 270 degrees rotate


See similar question on https://superuser.com/questions/418985/can-handbrake-flip-rotate-a-video