I do receive random thread notifications that I replied a long time ago, and it's totally random.
I just think it's the way it is, I have to clear it every time I log in.
I guess just accept it the way it is. Or keep looking for a solution on google, it has to do something with the phpBB software.
If you still want this thread reopened PM me, but it's no help really, there's a solution not to receive notification and if it's not working I couldn't find an alternative way for myself, even after googling the problem multiple times.
Or.. report it as a bug I guess?