Guys!
Please try this video (sfw) https://www.youtube.com/watch?v=Iqxbbiuqvag and tell if you have strange bright artifacts on white part of the video while in FULLSCREEN mode (not occurring in smaller player size).
I've just noticed it on my girlfriend's rMPB - she's using stock safari and is on 10.11.5 but she's NOT having youtube closing tab issue.
Anyway, the problem has been described on f.lux app forums and people have realized it is not the app issue but mac video driver (intel?) problem.
For me - as I'm using html5 converting plugin for Safari the problem of artifacts does not occur. (CORRECTION - artifacts are visible when video scrolling bar disappears!!!) photo here - notice the strange squares on white field (much brighter than other parts):

It also does not occur on opera (which has some drivers built in I believe, as it plays videos that require Silverlight plugin in other browsers without it).
My theory is: Apple has updated the intel video driver with ElCapitan (Yosemite must have had older version of the driver as our closing tab issue does not exist on Y.) and the driver is totally screwed up. Don't know if we need to blame Apple or Intel.
Correct me if I'm wrong but that's the only explanation I can find for that.