I use flux on a Macbook Pro Retina (Retina, 15-inch, Late 2013, 2.6 GHz Intel Core i7, OS X 10.9.5). When I use application based on java (ex. ImageJ, MATLAB) while flux modifies monitor color, a window which opened by the application blinks at several ten seconds. I like f.lux, but this phenomenon is so annoying that I quit f.lux. I'm not sure whether this kind of problem is common or not, and also whether you notice this kind of phenomenon. Anyway, I'm very happy if this will be fixed. Thanks.