I know this works because I get the notifications no matter what e-mail address I put in. So they are either getting dropped by your ISP, getting moved somewhere by your mail client, or the fact you have so many might be why you don't get any.
Like I mentioned before, I don't get notified on all new replies, I don't have it set to notify me on every topic I post in and I get all post and board notifications.
Before it was a path and permissions issue. The software is the same now, the only change is the server, which is setup correctly (otherwise I and others would not get the notifications). Since only the server has changed, which also means the IP, I am leaning on your ISP dropping them or your e-mail client thinking they are spam.
Earlier I mentioned no matter what e-mail address I use. What I mean is I now have it set using a gmail account, and I know gmail has strict filtering. So if it works there it should work almost anywhere unless someone (isp or service) is dropping all e-mail they think is spam.