Why are Notifications displaying only on one interface?
Notifications, Profile/Staff Accounts, Interfaces
Sending notifications are tracked at the site level to a specific account, rather than at the interface level.
While notifications are generated by the interface, the system passing them on to the user (agent) is simply watching the IDs of the notifications without respect to the interface they came from and seeing if they have been sent.
Another factor to consider here is the caching system. Logging in and out of the two interfaces, you are still dealing with the same set of cached data. All notifications will be passed to the first interface the user has logged into. The system will keep track of the notifications that have been seen by the user. When the user is logged out and logged in again they will only receive notifications that have not previously been delivered while logged in.
For more information, refer to these related resources:
Answer 1835: Staff notifications and email sent to staff
Answer 2389: Broadcasting a notification to other staff members