Since the new site started, the email notifications are still sent when I get PM's, but when I try to go to the address listed it now says that I am not logged on. Most of the time I am logged on. I can view them by going to PM from inside the board.

Is there something I am doing wrong here?

 

yes, the domain at which you are cookied is different than the domain in the e-mail.

all e-mails will have the www.s2000international.com, while you are currently logged in (cookied) at a different one. Such as www.s2000online.com.