Eating burned pancakes or toast is probably not harmful, but nobody really knows since burned toast isn't high on the research agenda.
One potential worry is a class of chemicals called acrylamides, recently established as probable carcinogens. Perhaps this is what you read about in the magazine article. Acrylamides are found in starchy foods exposed to high cooking temperatures, such as potato chips or French fries. Theoretically, acrylamides could be a problem in burned toast, too.
If you're worried about it, scrape the burned stuff off your pancakes. But, so far at least, there's not much evidence that burned toast is a health hazard. When I heat my whole wheat tortillas on my stovetop, I acutally like them to burn a little bit because I like the burned crispy parts. I guess we'll both find out in the future whether eating burned tortillas and pancakes is harmful.
Your peanut butter "panwich" sounds wonderful!