Something got messed up with scaling/native in this release. My C41 is hooked to a 1080p Sony LCD, has been since installation in May. The C41 has been set to "native" with all resolutions checked. This weekend watched a FOX (720p) show from recordings and it was "zoomed out" with a black border all around. I figured the local station could have done that by themselves but fiddling around after the recording ended, any live 720p broadcast was doing the same thing. Definitely a new behavior. Set to non-native, 1080i/p only and things are back to "normal"ish.
I started a thread about a similar bug where I was watching a 1080p 24hz PPV movie and then when I go back to 1080i broadcast HD it gets stuck at 24hz so its "jerky". I reboot then it gets stuck at 480p @ 60hz. Which could be similar to what you are seeing (since 480p would have black border all around).