You've probably already figured this out but here it is nonetheless:
Updating to Windows 8.1 enables by default a display scaling to 125% to enlarge icons for better readability (useful for tiny laptop screens with crazy high resolutions) which is why Windows thinks it's at its native resolution of 1080. However, GeForce Experience is unaware of this change and displays the resolution at something lower to adapt to the scaling.
The simple solution is to go back to the screen resolution display change from right clicking on your desktop and select "Make Text and Other items smaller or larger" and set the scale from 125% to 100% and voila! Your GeForce Experience should now be set to 1080p.