I am not getting popups/notifications for some replies
Some replies are directly going to previously read section. It happened couple of times now, I didn't get notification for these two replies, I thought may be I had my browser running in the background. But it happened again for these, replies. I did get notifications for the replies posted in between the mentioned replies.
I browse tildes mostly on mobile using Hermit. One can get notifications on your mobile from hermit lite apps by adding a url and a css selector, I used tildes.net/notifications/unread as the url and [div.logged-in-user-info:nth-child(4)] as the css selector. I did get notification (on my mobile) for couple of times but most of the time I didn't so I deleted the web monitor. It should be noted that I didn't know what I was doing. So how do I fix this? :(
My guess is that when hermit checks for new messages at the unread URL, it triggers' Tildes automatic "mark as read" functionality, and hence you don't see the messages when you browse in the interface. I'm not personally knowledgeable about Hermit, but as a temporary workaround, you can go into Settings and uncheck "Automatically mark all notifications read when you view the Unread Notifications page". This should prevent Tildes from dismissing any notifications without you explicitly telling it do so.
But, I didn't get notifications for replies posted even after I deleted the web monitor on Hermit. I did get yours though. :\