Mate, It depends on what you are using to play the files.
Most hardware and software players will allow you to "DOWNMIX" 5.1 to stereo and that is why I always use the 5.1 sound as it is the best supported and because I then have two choices.
1. When I am just playing through the TV, I have the "DOWNMIX" on and all plays fine.
2. When I switch my surround sound system on and route the sound through there, I have genuine 5.1 sound.
If you only encode to stereo, you are not future proofing yourself if you put in a surround system.
In your situation, I would be investigating the "MUDDY" sound as usually this can be resolved by settings on the player or on the TV.
Hope this helps.
