I've also noticed those extra tiles below Discovery's cockpit windows on the righthand side, in many of the photos I've seen of her, both in service and retired, and I've also wondered why they were there.
I actually use those distinctive tiles to help me to identify Disco in pictures where I can't quite make out her name, such as long-distance launch or landing shots, and when I'm downloading Shuttle photos, even close-up ones, I always know that it's a photo of Discovery when I see those distinctive tiles, even if the photo hasn't downloaded enough to let me read her name.