To rule anything out on my end, I went by Comcast and picked up a new receiver and am replacing the actual cable that goes from the wall into the receiver. I highly doubt it's the cable but I'm ruling everything out so they can't waste my time telling me to do stuff I know won't work. In any case, I'll post an update on Friday. That's when SG-1, Atlantis, and Battlestar Galactica air and that's when I would notice it. I also highly doubt this, but am just mentioning it to rule it out. Would modifying the audio settings on the receiver do something like this? I changed it to where there is no audio compression. Also, and like I previously mentioned, I have only noticed this on the SciFi channel.
Edit: Sorry, I forgot to answer your question. No, I am not using VOD.