This is normal with today's monitors. It's just the way they are. It doesn't have anything to do with software like f.lux. Stand up once and look at your monitor from that higher height and then crouch down and look at it. You'll see what i mean.
Thanks for your note! This is a tricky use case (for the sometimes early birds). If you're seeing a bright screen first thing in the morning, you can push your sleep timing earlier, so we are trying hard to get it right.
You want to wake up and use f.lux in daytime mode before the sun rises (and before your normal wake time), have I got it right?
@auntialias hey hi! Deleted my earlier incorrect response - 10.8.5 doesn't listen to us when we clear the notifications so this is a bug that's here to stay. You can turn off the notifications from the f.lux menu (just uncheck backwards alarm clock). Sorry for not having better news.
The ones before bed? It's like this: Open the f.lux settings menu (to the left of your system clock), then under options, just uncheck "Backwards Alarm Clock" and if you'd ever want to use them again, re-selecting it will re-enable them.
Which operating system are you seeing the problem on, and which video card does your machine have? This should be better in 10.10 for most video cards, they fixed a lot of bugs. And can you tell me what time of day the jumping happens - is it only when f.lux is transitioning?