Graphics issues with f.lux on 2012 MacBook Pro

[_Ties]

I recently installed f.lux on my MacBook Pro, and so far I really like the software. Unfortunately, around the same time I installed f.lux, I began to experience som graphical glitches. I'm not 100% sure that thees are related to f.lux, but I wanted to post about it here anyway. Worst-case scenario I can rule out f.lux and continue my trouble shooting.

The exact symptoms:

It started a couple of day's ago, when I woke my macbook pro from sleep.
The screen turned on with a sort-of pink and white pixeley oval instead of the normal login prompt. This stayed op for a bit under a second, than the screen flickered, and showed my login screen as normal.
This morning I noticed one pixel flashing a light green instead of dark gray at the bottom of the position indicator of my pasword prompt at lockscreen. (when the position indicator was visible, everyting was normal, but when it flashed to being invisible, the pixel turned light green.)
Just a minute ago I noticed a pink square-ish area in my menu bar, covering up the skype icon, and part of the f.lux icon. This went away as soon as I clicked on it.

The MacBook Specs:

MacBook Pro (13-inch, Mid 2012)
OS X 10.11.1 El Capitan
2,5 GHz Intel Core i5
8 GB 1600 MHz DDR3
Intel HD Graphics 4000 1536 MB

The reason I expect f.lux may be at least related to this issue, is that when I wake my laptop in the morning, the laptop wil turn on normally (as in at is normal daytime color temperature), and after a bit under a second the screen wil flicker, and turn on again with the orange glow created buy f.lux, which will than fade away in a few seconds, like it's supposed to do since the sun is up. This feels very similar in timing to the pink and white oval that appeared a few day's ago.

I read on the FAQ page that some MacBooks can experience some issues related to switching from the intel graphics chip to a dedicated graphics chip, but my laptop doesn't have a dedicated graphics chip, just the intel built-in HD 4000 chip. so that shouldn't be an issue for me.

Could this be caused by my laptop is struggling to run f.lux? And has anyone else experienced similar issues? Or is this totally unrelated to f.lux?