My notifications stopped too. My older notifications even got deleted from the notifications bar(that orange thing).
I used to get notifications from replies to my comments on other wordpress sites. Some don't even appear in my 'comments I've made' section.
I've tried it in multiple browsers but the problem still occured.
I've checked if I was logged in when I posted the comment, I was logged in. So it should be possible for WordPress to notify me of any replies. Going into the comments I've made section isn't the most clear way of viewing new replies.