I believe this occurred due to case-sensitivity of the installer class names, resulting in the class responsible for moving the stub-phrases from not being recognized.
The case of the respective class has been updated, and the upgrade log for it reset, in the next build. Starting in the next build, the phrases should be successfully moved to the main VaultWiki add-on during the main add-on's installation or its next full upgrade (to 4.1.0 Beta 3 or later). Thereafter, the navigation phrase would not be removed by uninstalling the stub.
Any currently affected installations, or any installation that runs the next build but uninstalls the stub before the phrases can be moved, would be automatically fixed at the next VaultWiki upgrade anyway. You could also re-install the phrases manually by using the "Run Upgrade Script" option even while you are already running the latest release.