About blinking window
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.
We install a system profile every time we make a "major" change, to ensure your dual GPU mac can switch video cards without it being noticeable. Some apps also listen to this change and try to update their UI.
Since it sounds like Java is doing something very expensive, I recommend you disable our profile writer, using the prefs on this page ("disableProfile"):
There may be some flickering if your machine switches GPUs but it's preferable to anything taking 10 seconds.