I haven't disabled it from the flux app, if that is what you're asking. As I mentioned, it works well when the cursor is hovering above a link. When it is not above a link, then it instantly becomes brighter and harsher - however, not as bright as when it is turned completely off. This happens whether or not I am in fullscreen mode, but if the window is not fullscreen, it is only the Chrome window that has this problem - the rest of the screen stays nicely reddish. I also just noticed that the problem doesn't seem to happen in tablet mode. When it is in tablet mode (ie rotated vertically), f.lux seems to work fine and there is no flickering at all, with Chrome or anything else.
EDIT: The chrome window also seems to flicker when I disconnect the surface type cover.