Actually I believe these problems are fairly common. I've seen them mentioned before and I experience them myself. I think it has to do with integrated vs discrete graphics in Mac laptops.

Disabling transparency in the accessibility options used to fix it, but it doesn't anymore.

I'm very much hoping that Apple will include this functionality in the next major release of OS X as f.lux has historically had trouble keeping up with OS and hardware updates.

A quick scan of the F.lux forum itself and the six or seven HN articles posted here in the past 90 days shows lots of people having issues. It's really not an easy problem because it's trying to do something that operating systems aren't great at and don't really give you a clean approach to tinker. And video drivers are some of the worst code out there. But I've used this thing off and on for years and it's always been glitchy. If you follow Lorna's Twitter you'll see she rants about all the lights in the house going nuts on occasion, too.

I believe this is a known issue, I have the same issues on elcap

"I couldn't be bothered to Google the problem, but based on my sample size of 1, I think your problem doesn't exist"

Thanks for that useful comment, man.

I had the exact same issue for several months until one day it abruptly stopped happening without me (knowingly) changing anything related to it.

I don't think so – this happens for me as well.

This has started happening to me this week, and it is getting worse. In fact, I just opened the laptop, and the screen flickered for 10 seconds---worst yet.

I have noticed the same problems.