I solved it. The problem was not the f.lux itself, but in so called Pixel dot-inversion. I can't say i understood right how it works, but briefly all LCD monitors are flickering on some brightness\contrast values. For example my IIYAMA flickers like mad at 79 and 81 brightness but goes smooth at 80. When i acitvate f.lux i get flickering at 3450, and 3350, but 3400 is perfect. There are also some monitor settings that make your screen flicker.
There's a visual test for that http://www.techmind.org/lcd/dotinvrgb2lb.html and an article that explains all this. I finaly understood why i had everything back to shape when i did windows restore.
Took me some time to google all this out. Maybe this will help someone having the same problem.