I did the same and solved the problem!
I had an adjustment layer with Brightness & Contrast blended with the video track wich had much more effects (MagicBullet Looks, Lumetri color, Warp stabilizer, etc.) and in some cases some masks.
I’ve almost panicked since I’ve workded all day at this color correction and my director was expecting a sample.
Worked just fine after I selected Remove flicker.
Thank you so much!
P.S.: I have Premiere CC 2015 on Mac 15′ Retina Display