Solution
In LabVIEW 2025 Q3, the Nigel AI Advisor is introduced and assigned the default shortcut Ctrl+Shift+N.
As a result, this shortcut key is not saved after each LabVIEW session.
To save Ctrl+Shift+N for the Navigation Window or any other feature, you must first reassign the Nigel AI Advisor shortcut to a different key combination. Refer to the below image on setting up Nigel AI Advisor shortcut key.
Before (default shortcut for Nigel AI Advisor):

After changing Nigel AI Advisor shortcut to Ctrl+Shift+P:
