I have this issue too. I am 10.10.5 OS and Safari 9.1 . I ran all my updates through and got some kernel panics but now seems ok. Safari, however, still think I won't accept cookies. Even though there are clearly the cookies from the websites which say it's not accepting them, in the cache. The Social Media sites and Linkedin are affected, all except one, and I also can't click on any other buttons, like expand search options, in google, for example. I have migrated to firefox, but feel somewhat naked without my extensions. I did also try toggling those off but it didn't change anything.