HD feeds are already mpeg encoded before broadcast. Encoder settings are only for analog feeds, where the card's onboard chip has to encode it to an mpeg stream.
Ok, that explains it. I am accessing only digital TV. I was mainly looking for a way to reduce the size of the recordings. A 30 minute show (HD or SD) is taking 6-7GB which seems like a lot for SD shows like The Simpsons. I guess I will keep looking.