It probably doesn't help that it has bugs. Sometimes my netbook will go through a horrifically jarring transition full of banding and a very obvious change in tone, it seems like sometimes flux gets a little stuck and then rapidly catches up.
Flux on my MBP is if anything even less predictable.
I also found when moving to my netbook to my MBP that I had to make very big changes to how much flux could change the colours - I have no idea what makes my previous settings so annoying on this computer, there's too many diferences between them to be sure.
On my MBP I completely ignore their recommended settings for lighting type. I picked the tone by adjusting the settings until it didn't feel like the light from my screen was physically attacking my eyes, which required a surprisingly small change in colour.