Transcode audio only for >2 channels

In order to eliminate a slight audio stutter on my Samsung 32D5000 I have found that transcoding to stereo audio works best. In doing so I lose the ability to jump to a certain time in the movie. Some files are already 2.0 so there is no need to transcode them and thus I can keep ablity to jump to a certain time. I have not found a way to only transcode audio for streams that have more than 2 channels. Can anyone help?

Thanks