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Are you saying PM pop up notifications are not working or that the Email Notification for replies hasn't been working? It can take up to fifteen minutes for a PM notice to pop up but usually it is much faster then that.
If the PM notifications are working for one person then they are working for the entire server. So this must be something they are doing-like perhaps clicking on links before the page finishes loading. It will only try to notify you three times so one click into a forum, one into a thread and one more could make the system think it notified someone and that is why they didn't get it. Time zones have nothing to do with notifications though silverginger. That only has to do with the way they see things on replies and how the log records their activity.
PM notification wasn't working for me, as well as a couple of other mods I'd sent PMs to. One of them got notified just a couple of hours ago, nearly 24 hours after the PM was sent! I'd sent a PM to another member, who doesn't seem to have been notified yet.
It, however, seems fine now; I received a PM an hour or so ago and was notified.
Is there a firewall or some other system interfering with the browser's ability to have a pop up notification? Like a pop up blocker? If you can leave usernames (whisper if you like) I can try to log in as them to test receiving it for them by sending a PM to the name to see if it notifies me upon logging on on the tcf board.