I'm a pretty big fan of watching shows after they start while recording them so I don't have to deal with the commercials. I noticed that one time while watching a recording I edited the cut point, but when I got to the point in the program that I was editing the program earlier, the recording was jumbled for the length of time that I was editing the cut point. Can anyone think of any reason why this would be? I thought the mpg wasn't edited at all when the commercials were being marked, just the positions added to the database.

No. Unless specified (the default), commercials aren't touched at all, just marked.