Rear projections, by design, must overscan the image about 3-5% in order to obtain what would be called pixel-perfect (and not shrink the original image). By shrinking 1080 to fit a RP, your text on desktop will become blurry. See if your TV has the mode 'just scan'. That is Samsung's pixel-to-pixel option. You would then set your CCC to 0 overscan. If correct, the corners of your desktop should be cut off and you should barely be able to see the start menu button, but text will be clear and easily read.
I own a Samsung HL67A750 with HDMI going through a Denon 990 first. I lose about 2% of my screen to achieve 'just scan'. I have a possibly similar issue as you in Media Center. Sometimes when I turn the TV and Receiver on, my Media Center screen will shrink to a smaller resolution. My TV will still report it as 1920x1080, but it's in the center of my screen with black bars all around it. I get Media Center to fix itself by hitting the windows key on my keyboard (which brings the desktop to the foregound). The resolution then corrects itself. When I then hit the start button on my remote to bring MC back into the foreground, MC stays at the correct resolution.
This issue did not start occurring for me until I introduced the Denon 990. EDID override did not help. I plan on using EventGhost so I can program the Windows Key as part of the activity startup on the Harmony remote.