As one of the first subscribers to the site, first let me say that the new design is much much better than the previous one.
However, I am not writing this message just to praise this site. I have also been one of the first subscribers to the email notification feature. Before the recent revamp (when you decided to no longer have message threads on the same page, but to have messages linking from one to the other), the email notification worked perfectly, and I could always go to messages I haven’t read.
Now, after the revamp, I am not getting email notification for all the messages. I do not know if it is only me or if it is a global phenomenon here on the site. I sometimes find myself going to a middle of a thread, without any messages in my mailbox linking to the previous (or next) messages! I may have missed a thread or two this way – but I do not know.