NoteTracker running is completely separate from the HUD, though the notes are displayed there the notes being taken can't be affected like that.
Please play another session and then send us your PokerTracker4.log file - that will show if any NoteTracker notes were taken and give us a considerable amount of extra information about what is going on within PT4. You can find this file by clicking File --> Show User Data Folder in the main PT4 window - the file we need is the text file called PokerTracker4 that's in the folder that appears. Send us the file via our
support system and we'll look into this and get back to you.