Use the console to rotate the video maintaining the properties:
$ mencoder input_video.mp4 -o output_video.mp4 -vf rotate=1 -oac pcm -ovc lavc
Here the audio channel is processed with pcm (-oac pcm) and the video chanel is coded using libav library (-ovc lavc)
An example of shell script using mencoder could be:
#! /bin/bash
if [ "$#" -eq 2 ]; then
echo "Rotate video '$1' and store it as '$2'"
mencoder $1 -o $2 -vf rotate=1 -oac pcm -ovc lavc
echo "Video was processed!"
else
echo "Error: Lack of arguments."
echo "The correct use is: rotate_video.sh <input_video_name> <output_video_name>"
fi