Hm. That sounds like something more complex than can be diagnosed via comments to a news post; open a support request with a link to the post that you're not getting notifications for and we'll see if we can poke at it a bit. (It will almost certainly take a while, as weird edge cases like that take time to look into and requires somebody with database access, which is like two people.)

....although, actually, if the problem only started in the last few hours, it's because I posted this post. When news posts get posted, the entire notification system backs up for a while while it chews through all the notifications it has to send out.