~snip~
So this concludes that the issue wasn't from the forum, but from the email service provider.
Maybe because all the email notifications for replies have the same subject/title (ex. Re:Thread Title) unlike new threads with different titles, your email service mistakenly identifying them as spam.
I can't comprehend "wired experience" though.
Well yes, we can confirm that there were no issue from the forum side. It must be the email client. I am using gmail which I guess most of us do. I think it could be the same email subject. My setup was the same from long time and those post notifications were working all those days except yesterday. Although I have manually marked all these emails as Not Junk and since then I am receiving them in my inbox again.
Anyway, since it's not forum issue which we can confidently say, I am locking this topic.
Cheers everyone.