Based on that information it's possible your database cache needs to be rebuilt. If your database isn't very large click "Database -> Database Management", select your database then "Rebuild Cache -> Full Cache Rebuild". Be prepared for this to take a considerable amount of time if you have a large database and/or a slow HDD and it could fail completely if you do not have much free disk space. Make sure that your computer does not power itself off or go to sleep while it's running or you will need to run it again from the start.
If that doesn't fix it
enable logging, reproduce this problem with your popups and then send your log file to us in a
Support Ticket. You can access the 'Logs' folder with the log file by clicking 'File --> Open User Data Folder' in the main PokerTracker 4 window and the file we need is the text file called 'PokerTracker4' or 'PokerTracker4.log' that is in that folder.