Since it only affects live/recorded tv, my first thought was that it might be related to the 29/59 issue, but if it happens on all of the live/recorded TV then that seems unlikely. (But if you're inclined to confirm, while watching a TV show you can hit 4-1-1 on your keyboard (as if changing the channel to 411), then immediately hit CTRL+D and that should bring up the WMC diagnostic screen. you can use your left and right arrows to navigate from one page to another. If you find the framerate value, and it seems to be jumping back and forth between different values, in-time with the dropped frames on your screen, then it is likely the 29/59 issue. There are already several threads on here that relate to is so I won't go into too much detail about it here.
If it's not that, then I'm guessing it has something to do with the MS MPEG-2 decoder. I've never tried it, but I'm told it's possible to use a different MPEG-2 decoder in WMC, which might be a viable fix for you depending on a few things. My understanding is trhat Comcast doesn't flag any of their content as "Copy Once" except for premium channels. So if you don't subscribe to HBO or any premium channels and you don't plan on ever ordering Pay-Per-View then you could theoretically swap out the decoder if that fixes your problem.
RAID protection is only for failed drives. That's it. It's no replacement for a proper backup.