Since you recieve notification for some, and not for others, it might be a bug, or a misconfiguration of the settings.
On your profile->notifications and email
For topics and boards I've requested notification on, notify me of: (that is for those threads you've clicked the "notify" button):
"Moderation only if I started the topic"
This seems as the default option, but seems to mean you'll only recieve notifications if you were the one starting the topic.
Try selecting:
"Replies and moderation"
It's not that I use that functionality at all, but your problems might be due to that.