Not sure but I can think of some things:
1) You only get notifs for things you mark as "Now Reading" or "Already Read". You do not get notifs for those in "Want to Read"
2) You only get update notifs 2 times a day. Im on Eastern USA time (EST) and my update notifs come at 10am and 10pm. So if a story get a new chapter uploaded at 1pm, I wouldn't get the notification for that until 10pm that same day.
3) When you're marking a story as "Now Reading" or "Already Read" (so that you get notifications), there is a checkbox under the rating that says "Subscribe this manga". For me, it's always checked by default so I never play with it. But maybe check if the stories you don't get notifications for have that checkbox marked or not.
Why do some updates.. despite adding them to the list doesnt show in my notifications?? （￣へ￣）