This occurs on all Creative Finishing applications (Flame, Smoke, Lustre).
When generating proxies, the application removes pixels from the full resolution files in order to fit it the new resolution frame format. While doing this, the application rebuilds the frames in order to get the closest results between the Full resolution files and the Proxies.
Since there is no 1 to 1 parity for the pixels between the Full resolution files and the Proxies files, the pixels used by the keyer on both resolutions will not have the exact same color data and therefore will exhibit slight color differences.