The way notifications work - you only get the first reply after your visit to the thread. This is a "precaution" feature on the bulletin board software so that it does not flood your inbox with every reply (in case there are 50). Once you visit the thread, the counter is reset and will notify you again once there is a reply, so on.
So, if you have a couple of threads that are NOT getting notifications, just visit them, and next time there is a reply, you will be sure to hear.
Alternatively, you can also subscribe to entire forums to be notified when a message is posted. Just click on the subscribe button when viewing the specific forum. I found this to be a more reliable method in case I don't check out every thread I get a notification about....
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