Here's something for thought as well...
I'm currently running the beta 8.4 of version 6.0, and I love the program on a whole. Sending e-mail confirmations was one of my favorite features, but like you, there was a problem getting it to work. I could, however, register for my own board, and it would send me an e-mail response like it was supposed to. Couldn't quite figure that one out.
Anyway... to the point.
My personal ISP is MSN. I'm hosted on addr.com. I've just been told that when I send mail using addr.com while connected at the same time to MSN, my mail will NOT go out. It's a spam prevention tool that MSN has recently implemented. (While connected to MSN, a user can supposedly send bulk e-mail thru their connection w/o them knowing it. If you're forced to use their SMTP on your e-mail, then they can track you down... if you're a spammer)
The bottom line... I don't know if this has anything to do with the problem on my user registrations or not, but I will soon find out. I've only been informed of the problem as of yesterday! If anyone has any suggestions, please let me know.