f.lux does not have any permanent effects once it's uninstalled.
There is one thing about updating your Intel driver. Intel drivers frequently add a power-saving feature called "DPST" that causes a visible effect. I always turn it off through the "HD Graphics control panel". If you have that control panel, look in "power" and "battery" and see if you can turn off "Display Power Saving Technology".
If that's not it and you think it's related to f.lux, please send a video to support at justgetflux.com