I am having the exact same problems. I see that other have been having this problem yet no one seems to be alarmed about it. I find it interesting that something so basic as setting up forums does not seem to work properly without a bunch of custom code, hard-to-understand menu settings, and ultimately code that does not work.
I did get things to work. I had to manually fix the code. I could not wait for anyone at BuddyPress since they do not seem to be here helping out. I would provide you with the fix, yet I rewrote a bunch of the code since there were many things that I found that needed to be fixed to make our site to work.
Ok, I did what your asked me to do last night. I deactivated all the plugins and then activated the BuddyPress default theme. I get the same results. I sign up to be come a new member and I do not get the confirmation email. I have attempted to sign up with a number of email accounts that I have and nothing is going into my spam folders or my inbox.
Recently we have updated to the new BuddyPress 1.6.2. Ever since the upgrade, the confirmation email is not going out to members attempting to register as new members. Our site is http://rotarymeansbusiness.com/. We now see that others are having this problem. We did not have this problem before the upgrade. We also use the plugin “Buddypress Pending Activations.